Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008755.1 Hibiscus syriacus cultivar Beakdansim tig00111847_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: 3030620
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 14
Found at i:967780 original size:42 final size:39
Alignment explanation
Indices: 967695--967790 Score: 122
Period size: 42 Copynumber: 2.4 Consensus size: 39
967685 TTTGTTTTAT
*
967695 TTTTATTTTTATTTTTATTTTTTTATTTTTATTCATTTTG
1 TTTTA-TTTTATTTTTATTTTTTTAATTTTATTCATTTTG
*
967735 TTTTATTTTATTTTTATTTATTTTACCATTTTATTTATTTTG
1 TTTTATTTTATTTTTATTT-TTTTA--ATTTTATTCATTTTG
967777 TTTT-TGTTTATTTT
1 TTTTAT-TTTATTTT
967791 AGTGTTCTCC
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
39 14 0.28
40 10 0.20
41 1 0.02
42 25 0.50
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (39 bp):
TTTTATTTTATTTTTATTTTTTTAATTTTATTCATTTTG
Found at i:967825 original size:12 final size:12
Alignment explanation
Indices: 967808--967848 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
967798 TCCCTTTGTT
967808 TTTTTTTGTTCA
1 TTTTTTTGTTCA
*
967820 TTTTTTTATT--
1 TTTTTTTGTTCA
967830 TTTTTTTGTTCA
1 TTTTTTTGTTCA
967842 TTTTTTT
1 TTTTTTT
967849 ATATTTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 9 0.36
12 16 0.64
ACGTcount: A:0.07, C:0.05, G:0.05, T:0.83
Consensus pattern (12 bp):
TTTTTTTGTTCA
Found at i:967854 original size:24 final size:22
Alignment explanation
Indices: 967806--967850 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
967796 TCTCCCTTTG
967806 TTTTTTTTTGTTCATTTTTTTA
1 TTTTTTTTTGTTCATTTTTTTA
967828 TTTTTTTTTGTTCATTTTTTTA
1 TTTTTTTTTGTTCATTTTTTTA
967850 T
1 T
967851 ATTTAGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.09, C:0.04, G:0.04, T:0.82
Consensus pattern (22 bp):
TTTTTTTTTGTTCATTTTTTTA
Found at i:968353 original size:60 final size:60
Alignment explanation
Indices: 968269--968403 Score: 166
Period size: 60 Copynumber: 2.2 Consensus size: 60
968259 ATAATATGGG
* * * *** *
968269 TAAAAA-TATAGAAATGATTCCCTAATTATAAGACTTTACATTGTTAAAT-CTCTTGACTAT
1 TAAAAATTATA-AAATAATCCCCTAACTATAAGAAACTACATTGTTAAATCCT-TTAACTAT
*
968329 TAAAAATTATAAAATAATCCCCTAACTATAAGAAACTACTTTGTTAAATCCTTTAACTAT
1 TAAAAATTATAAAATAATCCCCTAACTATAAGAAACTACATTGTTAAATCCTTTAACTAT
968389 TAAAAATTATAAAAT
1 TAAAAATTATAAAAT
968404 GATCATTTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
60 59 0.91
61 6 0.09
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.36
Consensus pattern (60 bp):
TAAAAATTATAAAATAATCCCCTAACTATAAGAAACTACATTGTTAAATCCTTTAACTAT
Found at i:969375 original size:31 final size:31
Alignment explanation
Indices: 969317--969385 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
969307 TATTTGACAG
* *
969317 TTACAAAAGAATCATTAAATTTCTCGAACTA
1 TTACAAAAGAATCATTAAATTTATCGAAATA
*
969348 TTACAAAA-AATCATTAAATTTTATCGAAATG
1 TTACAAAAGAATCATTAAA-TTTATCGAAATA
969379 TTACAAA
1 TTACAAA
969386 TTATTATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 10 0.29
31 24 0.71
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (31 bp):
TTACAAAAGAATCATTAAATTTATCGAAATA
Found at i:975494 original size:39 final size:39
Alignment explanation
Indices: 975440--975517 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
975430 AAAATAATTG
975440 GTGTGGTGATGTGATCCTACTCTTACACCTTATACTCTT
1 GTGTGGTGATGTGATCCTACTCTTACACCTTATACTCTT
975479 GTGTGGTGATGTGATCCTACTCTTACACCTTATACTCTT
1 GTGTGGTGATGTGATCCTACTCTTACACCTTATACTCTT
975518 CATCTTGCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (39 bp):
GTGTGGTGATGTGATCCTACTCTTACACCTTATACTCTT
Found at i:975941 original size:30 final size:30
Alignment explanation
Indices: 975869--975956 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
975859 TCTTTATTAT
** * *
975869 ATGTTTATGCA-TCATTCTTTAGCTCTTTCT
1 ATGTTTATGCATTCA-TAATTAGCTCATTCC
*
975899 ATGTTTATGCATTCATAGTTAGCTCATTCC
1 ATGTTTATGCATTCATAATTAGCTCATTCC
* *
975929 ATGTTTATGCATTTATAATTATCTCATT
1 ATGTTTATGCATTCATAATTAGCTCATT
975957 TGCATCATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 47 0.94
31 3 0.06
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (30 bp):
ATGTTTATGCATTCATAATTAGCTCATTCC
Found at i:976317 original size:21 final size:21
Alignment explanation
Indices: 976291--976362 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
976281 TGTCACTAGG
*
976291 TACCTAGCTAGTTATCTACAC
1 TACCTAGCTAGTTAACTACAC
*
976312 TACCTAGCTAGTTACCTA-AGC
1 TACCTAGCTAGTTAACTACA-C
* *
976333 TACCTAGCTAGCTAACTCCAC
1 TACCTAGCTAGTTAACTACAC
*
976354 TAGCTAGCT
1 TACCTAGCT
976363 TCCATGACTC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
20 1 0.02
21 42 0.95
22 1 0.02
ACGTcount: A:0.28, C:0.31, G:0.12, T:0.29
Consensus pattern (21 bp):
TACCTAGCTAGTTAACTACAC
Found at i:977378 original size:22 final size:21
Alignment explanation
Indices: 977353--977393 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
977343 AAGAAGAAAA
977353 CAACAGAAAAAAAGACTTCATT
1 CAACA-AAAAAAAGACTTCATT
* *
977375 CAACAACAAAAAGAGTTCA
1 CAACAAAAAAAAGACTTCA
977394 AAGAATCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.56, C:0.20, G:0.10, T:0.15
Consensus pattern (21 bp):
CAACAAAAAAAAGACTTCATT
Found at i:981587 original size:17 final size:17
Alignment explanation
Indices: 981565--981606 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
981555 GTGTTTGTTG
*
981565 CTCGAACGAGAGATTT-T
1 CTCGAAAGAGA-ATTTCT
981582 CTCGAAAGAGAATTTCT
1 CTCGAAAGAGAATTTCT
981599 CTC-AAAGA
1 CTCGAAAGA
981607 AAGGGAAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (17 bp):
CTCGAAAGAGAATTTCT
Found at i:984410 original size:26 final size:25
Alignment explanation
Indices: 984380--984429 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
984370 AATCCCAAAT
984380 ATTTAATTTAAATT-AAATAAATAAAG
1 ATTTAA-TTAAATTGAAAT-AATAAAG
*
984406 ATTTAATTAATTTGAAATAATAAA
1 ATTTAATTAAATTGAAATAATAAA
984430 ATCCTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTTAATTAAATTGAAATAATAAAG
Found at i:986315 original size:13 final size:13
Alignment explanation
Indices: 986297--986325 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
986287 AAAAAACATA
986297 AAGGAGAGCATTG
1 AAGGAGAGCATTG
986310 AAGGAGAGCATTG
1 AAGGAGAGCATTG
986323 AAG
1 AAG
986326 AAGGTTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.38, T:0.14
Consensus pattern (13 bp):
AAGGAGAGCATTG
Found at i:993672 original size:138 final size:138
Alignment explanation
Indices: 993362--993753 Score: 475
Period size: 138 Copynumber: 2.8 Consensus size: 138
993352 GGTGTTGTTC
* * * * * * *
993362 CAACTCCTTATGGGATGGAAACAAGCTAAGGTTAAACAAGTTCTTTTCATTATGAACTTTTTATC
1 CAACTCCATATGTGAT-GAATCAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTC
* * * * * *
993427 CCTTATCGGATGAATTCTTCTCATAATGAACTCTCCACTGGAAATGTTGATCCCTTGAGTGAGAT
65 CCTCATCGAACG-ATTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAGCCCTCGAGTGAGAT
993492 ATTGCTGATT
129 ATTGCTGATT
* * * * * *
993502 TAACTCCATATGTGATGAATCAAGTTAAGGTTGAACAAGATATTCTGATTATGAACTTCTTCTCC
1 CAACTCCATATGTGATGAATCAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCC
*
993567 CTCATCGAACGAGTTCTTCTCATTATGAACTCTCCACT-GAAATGTTG-GCCGCTCGAGTGAGGT
66 CTCATCGAACGA-TTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAGCC-CTCGAGTGAGAT
*
993630 GTTGCTGATT
129 ATTGCTGATT
*
993640 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCC
1 CAACTCCATATGTGATGAATCAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCC
* * **
993705 CTCATCGGATAC-ATTCTTCTCATTATGAACTATCCGCTATAAATGTTGA
66 CTCATC-GA-ACGATTCTTCTCATTATGAACTCTCCACTGGAAATGTTGA
993754 CTGGGTTTAT
Statistics
Matches: 216, Mismatches: 30, Indels: 12
0.84 0.12 0.05
Matches are distributed among these distances:
137 2 0.01
138 116 0.54
139 83 0.38
140 15 0.07
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (138 bp):
CAACTCCATATGTGATGAATCAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCC
CTCATCGAACGATTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAGCCCTCGAGTGAGATAT
TGCTGATT
Found at i:994250 original size:101 final size:99
Alignment explanation
Indices: 994097--994333 Score: 341
Period size: 101 Copynumber: 2.4 Consensus size: 99
994087 ATCTCATGAA
* **
994097 AAATTGATTTTAAGAAAAAAACATCTCAAGTGATAAATTTTGGTTTTGAGTGAAATGATTTCAAA
1 AAATTGATTTTAAG-AAAAAACATCTCAAGTGATAAATTTTGGTTTAGAGTGAAAAAATTTCAAA
* * *
994162 ATCTGTGTTCCAAG-GGAAACTATTTCAAAAAAATATG
65 ATATGTGTTCCAAGAGG-AACTACTTC--AAAAAGATG
* * *
994199 AAATTGATTTTACGAAAAATCATCTCAAGTGATAAATTTTTGTTTAGAGTGAAAAAATTTCAAAA
1 AAATTGATTTTAAGAAAAAACATCTCAAGTGATAAATTTTGGTTTAGAGTGAAAAAATTTCAAAA
994264 TATGTGTTCCAAGAGGAACTACTTCAAAAAGATG
66 TATGTGTTCCAAGAGGAACTACTTCAAAAAGATG
*
994298 AAATTGATTTTAAGAAAAACCATCTCAAGTGATAAA
1 AAATTGATTTTAAGAAAAAACATCTCAAGTGATAAA
994334 ATTTATCTTT
Statistics
Matches: 123, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
99 42 0.34
101 66 0.54
102 15 0.12
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (99 bp):
AAATTGATTTTAAGAAAAAACATCTCAAGTGATAAATTTTGGTTTAGAGTGAAAAAATTTCAAAA
TATGTGTTCCAAGAGGAACTACTTCAAAAAGATG
Found at i:1008319 original size:20 final size:21
Alignment explanation
Indices: 1008265--1008327 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
1008255 GATTCCCCTG
1008265 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
1008289 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
1008309 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
1008328 TACACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:1012171 original size:22 final size:21
Alignment explanation
Indices: 1012129--1012168 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1012119 GAGTTTGTTT
*
1012129 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1012150 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1012169 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1021651 original size:9 final size:9
Alignment explanation
Indices: 1021637--1021661 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1021627 TTTAGGGTCG
1021637 AATGGTTCC
1 AATGGTTCC
1021646 AATGGTTCC
1 AATGGTTCC
1021655 AATGGTT
1 AATGGTT
1021662 ACCCAGCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (9 bp):
AATGGTTCC
Found at i:1047703 original size:58 final size:58
Alignment explanation
Indices: 1047613--1047728 Score: 214
Period size: 58 Copynumber: 2.0 Consensus size: 58
1047603 ATTTAAAATG
*
1047613 AGCTTACAACTCATTAACACTTGTTTTAATTAGGGCAAGAGCGAGGGGAGACCTCCAA
1 AGCTTACAACTCATTAACACTTGTTTTAATTAGGGCAAGAGCGAGGGAAGACCTCCAA
*
1047671 AGCTTACAACTCATTAACACTTGTTTTAATTAGGGCAATAGCGAGGGAAGACCTCCAA
1 AGCTTACAACTCATTAACACTTGTTTTAATTAGGGCAAGAGCGAGGGAAGACCTCCAA
1047729 GGCCAAAGGC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (58 bp):
AGCTTACAACTCATTAACACTTGTTTTAATTAGGGCAAGAGCGAGGGAAGACCTCCAA
Found at i:1048485 original size:5 final size:5
Alignment explanation
Indices: 1048475--1049163 Score: 1179
Period size: 5 Copynumber: 137.6 Consensus size: 5
1048465 ATGTTTGTCT
*
1048475 GTTAC GTTAC GCTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1048525 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1048575 GTTAC G-TAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1048624 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1048674 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
* * *
1048724 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GCTAC GCTAC GTTAC GCTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
* * *
1048774 GTTAC GTTAC GTTAC GTTAC GCTAC GTTAC GTTAC GCTAC GCTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
* * *
1048824 GTTAC GCTAC GCTAC GTTAC GTTAC GTTAC GTT-- GATATAC AGATATC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC G-T-TAC -GTTA-C
** **
1048871 -TTTT GTTTGG GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC G-TTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1048921 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1048971 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1049021 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1049071 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1049121 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTT
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTT
1049164 GATATACAGA
Statistics
Matches: 655, Mismatches: 20, Indels: 18
0.95 0.03 0.03
Matches are distributed among these distances:
3 1 0.00
4 5 0.01
5 642 0.98
6 5 0.01
7 1 0.00
8 1 0.00
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (5 bp):
GTTAC
Found at i:1059688 original size:24 final size:24
Alignment explanation
Indices: 1059637--1059688 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
1059627 ATCATTTTTA
* *
1059637 TTTTACTTCTTTATTTTTGTATAG
1 TTTTACTTCGTTATTTTTGTATAC
*
1059661 TTTTACTT-GTTATTTTTGTTTACC
1 TTTTACTTCGTTATTTTTGTATA-C
1059685 TTTT
1 TTTT
1059689 TAGTGTTGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.13, C:0.10, G:0.08, T:0.69
Consensus pattern (24 bp):
TTTTACTTCGTTATTTTTGTATAC
Found at i:1070734 original size:22 final size:22
Alignment explanation
Indices: 1070706--1070762 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
1070696 ACCCAGACCA
* *
1070706 TTGACTTTAACCAGAGTTGATT
1 TTGACTTTGACCAGAGTTGACT
** *
1070728 TTGACTTTGATTAGGGTTGACT
1 TTGACTTTGACCAGAGTTGACT
1070750 TTGACTTTGACCA
1 TTGACTTTGACCA
1070763 AAATTTGAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (22 bp):
TTGACTTTGACCAGAGTTGACT
Found at i:1078463 original size:27 final size:27
Alignment explanation
Indices: 1078421--1078488 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
1078411 TTGTAGGAAT
1078421 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1078446 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
1078473 TATAAAGATATGATTT
1 TATAGAGATATGATTT
1078489 TGTAAATAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 7 0.17
27 33 0.82
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:1082229 original size:27 final size:27
Alignment explanation
Indices: 1082187--1082254 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
1082177 GTGTAGGAAT
1082187 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1082212 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1082239 TATAGAGATATGATTT
1 TATAGAGATATGATTT
1082255 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:1085368 original size:32 final size:32
Alignment explanation
Indices: 1085308--1085370 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
1085298 TGAGTAAGTG
* * * * *
1085308 TGAAATTATTTGTTTAATTTTTTTATTTTTTA
1 TGAAATTATTTATTGAATATGTTAATTTTTTA
1085340 TGAAATTATTTATTGAATATGTTAATTTTTT
1 TGAAATTATTTATTGAATATGTTAATTTTTT
1085371 TTATGGACAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (32 bp):
TGAAATTATTTATTGAATATGTTAATTTTTTA
Found at i:1086710 original size:59 final size:58
Alignment explanation
Indices: 1086641--1086754 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 58
1086631 ATGTTTGGTT
* * *
1086641 TTTCCTATTTAT-TTTTTGGATGAGTGTGATAAATTTTCATATTTTATTTAAATGAATG
1 TTTCCTATTTATCTTTTT-AATGAGTGTGATAAATTTCCACATTTTATTTAAATGAATG
* ** *
1086699 TTTCCTTATTTATCTTTTTAATGTGTGTGATTGATTTCCACATTTTATTTGAATGA
1 TTTCC-TATTTATCTTTTTAATGAGTGTGATAAATTTCCACATTTTATTTAAATGA
1086755 GTATGATAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
58 5 0.11
59 37 0.79
60 5 0.11
ACGTcount: A:0.25, C:0.08, G:0.13, T:0.54
Consensus pattern (58 bp):
TTTCCTATTTATCTTTTTAATGAGTGTGATAAATTTCCACATTTTATTTAAATGAATG
Found at i:1089316 original size:173 final size:170
Alignment explanation
Indices: 1089020--1089362 Score: 627
Period size: 173 Copynumber: 2.0 Consensus size: 170
1089010 TTTTAAATGT
1089020 TTAAGTGTTGATTAAATATCTTATTAAGGTGCTGGAATTTTATGTCATTAATGTGACATGATCAT
1 TTAAGTGTTGATTAAATATCTTATTAAGGTGCTGGAATTTTATGTCATTAATGTGACATGATCAT
1089085 AATAGTGAAGGGCTATAGGTTTAATGAAAAGTTAAGGTGATTTCTAGAAAGTATTCAAAATTAGT
66 AATAGTGAAGGGCTATAGGTTTAATGAAAAGTTAAGGTGATTTCTAGAAAGTATTCAAAATTAGT
1089150 GG-TTAATTAT-TATTTAGAAAAAGTTGAAGGGAGACAAA
131 GGTTTAATTATGTATTTAGAAAAAGTTGAAGGGAGACAAA
1089188 TTAAGTGTTGATTTAAATATCTTATTAAGGTGCTGGAAATTTTATGTCATTAATGTGACATGATC
1 TTAAGTGTTGA-TTAAATATCTTATTAAGGTGCTGG-AATTTTATGTCATTAATGTGACATGATC
1089253 ATAATAGTGAAGGGCTATTATAGGTTTAATGAAAAGTTAAGGTGATTTCTAGAAAGTATTCAAAA
64 ATAATAGTGAAGGGC---TATAGGTTTAATGAAAAGTTAAGGTGATTTCTAGAAAGTATTCAAAA
1089318 TTAGTGGTTTAATTATGTATTTAGAAAAAGTTGAAGGGAGACAAA
126 TTAGTGGTTTAATTATGTATTTAGAAAAAGTTGAAGGGAGACAAA
1089363 GGTAGTGCAT
Statistics
Matches: 168, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
168 11 0.07
169 24 0.14
170 43 0.26
173 54 0.32
174 8 0.05
175 28 0.17
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.36
Consensus pattern (170 bp):
TTAAGTGTTGATTAAATATCTTATTAAGGTGCTGGAATTTTATGTCATTAATGTGACATGATCAT
AATAGTGAAGGGCTATAGGTTTAATGAAAAGTTAAGGTGATTTCTAGAAAGTATTCAAAATTAGT
GGTTTAATTATGTATTTAGAAAAAGTTGAAGGGAGACAAA
Found at i:1092631 original size:21 final size:20
Alignment explanation
Indices: 1092602--1092642 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1092592 CGTCTTTCTA
*
1092602 TAATTAATTAAATAATAAAAT
1 TAATCAATT-AATAATAAAAT
*
1092623 TAATCAATTAATCATAAAAT
1 TAATCAATTAATAATAAAAT
1092643 AAACTTCTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
TAATCAATTAATAATAAAAT
Found at i:1098214 original size:20 final size:20
Alignment explanation
Indices: 1098189--1098235 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1098179 TGCTTATGGT
1098189 ACTATTGAGCGGCGCAAAGC
1 ACTATTGAGCGGCGCAAAGC
1098209 ACTATTGAGCGGCGCAAAGC
1 ACTATTGAGCGGCGCAAAGC
*
1098229 ACGATTG
1 ACTATTG
1098236 TATCTTTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.30, T:0.17
Consensus pattern (20 bp):
ACTATTGAGCGGCGCAAAGC
Found at i:1113956 original size:13 final size:13
Alignment explanation
Indices: 1113902--1113948 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
1113892 TACGTCATAA
1113902 ATTTATGACGCGC
1 ATTTATGACGCGC
*
1113915 ATTTATGACACGC
1 ATTTATGACGCGC
*
1113928 ATTTATGACGAGC
1 ATTTATGACGCGC
1113941 ATTTATGA
1 ATTTATGA
1113949 TGCTCATTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:1124242 original size:21 final size:19
Alignment explanation
Indices: 1124218--1124267 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
1124208 TTACATATCT
*
1124218 TTATTTTATCTTTATCTATTC
1 TTATTTTAT-TTTATC-AATC
1124239 TTATATTTATTTTATCAATC
1 TTAT-TTTATTTTATCAATC
1124259 TT-TTTTATT
1 TTATTTTATT
1124268 ATATTAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 6 0.22
19 1 0.04
20 5 0.19
21 10 0.37
22 5 0.19
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTTTATTTTATCAATC
Found at i:1128960 original size:46 final size:46
Alignment explanation
Indices: 1128904--1129553 Score: 719
Period size: 46 Copynumber: 14.2 Consensus size: 46
1128894 AAAATGAATT
* *
1128904 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATAAAAGGGTGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * * *
1128950 CATAACTAAAATGCGTG--ATGATGCATTAAGGTATGAAAGGGTGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
1128994 CATAACTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGT
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1129040 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG-
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * * *
1129085 CAT---T--AAGGCATGAAATGATGCCATAACTAAAATGCATGAAATGATG-
1 CATAACTAAAATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATGC
* * * *
1129131 CAT---T--AATGAATGAAAGGATGCCATAACTAAAATGTATGAAATGATG-
1 CATAACTAAAATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATGC
* * *
1129177 CAT---T--AAGGCATGAAAAGATGCCATAACTAAAATGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATGC
*
1129224 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1129270 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
1129316 CATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGA
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1129362 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
1129408 CATAACTAAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGA
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
1129454 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * * * *
1129500 CATAATTAAAATGCATGAAATGATGCATTAAGGCCTGAAATGATAC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
1129546 GATAACTA
1 CATAACTA
1129554 GAATTTACGA
Statistics
Matches: 547, Mismatches: 43, Indels: 28
0.89 0.07 0.05
Matches are distributed among these distances:
40 14 0.03
41 3 0.01
42 1 0.00
44 41 0.07
45 3 0.01
46 463 0.85
47 3 0.01
48 1 0.00
50 1 0.00
51 3 0.01
52 14 0.03
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (46 bp):
CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:1129217 original size:72 final size:72
Alignment explanation
Indices: 1129135--1129553 Score: 373
Period size: 72 Copynumber: 6.0 Consensus size: 72
1129125 ATGATGCATT
* * * *
1129135 AATGAATGAAAGGATGCCATAACTAAAATGTATGAAATGATGCATTAAGGCATGAAAAGATGCCA
1 AATGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
1129200 TAACTAA
66 TAACTAA
*
1129207 AATGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCA
1 AATGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
1129272 TAACTAA
66 TAACTAA
* * *
1129279 AATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATGCCATAACTAAAATGCATGAAATG
1 AATGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGG
1129338 ATG-CAT---T--
60 ATGCCATAACTAA
* *
1129345 AAGGCATGAAAGGATGACATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
1 AATGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
1129410 TAACTAA
66 TAACTAA
* * *
1129417 AATACATGAAAGGATG-CAT---T--AAGGCATGAAAGGATGACATAACTAAAATGCATGAAAGG
1 AATGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGG
1129476 ATG-CAT---T--
60 ATGCCATAACTAA
* * * * * * * *
1129483 AAGGCATGAAATGATGCCATAATTAAAATGCATGAAATGATGCATTAAGGCCTGAAATGATACGA
1 AATGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
1129548 TAACTA
66 TAACTA
1129554 GAATTTACGA
Statistics
Matches: 286, Mismatches: 26, Indels: 71
0.75 0.07 0.19
Matches are distributed among these distances:
66 84 0.29
67 17 0.06
68 6 0.02
70 6 0.02
71 18 0.06
72 155 0.54
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.21
Consensus pattern (72 bp):
AATGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
TAACTAA
Found at i:1129312 original size:164 final size:164
Alignment explanation
Indices: 1128904--1129387 Score: 768
Period size: 164 Copynumber: 3.0 Consensus size: 164
1128894 AAAATGAATT
* * *
1128904 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATAAAAGGGTGCCATAACTAAAATGCGTG--
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
* * *
1128967 ATGATGCATTAAGGTATGAAAGGGTGCCATAACTAAAATGCATGAAAAGATGCATTAAGGCATGA
66 ATGATGCATTAAGGAATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGCATGA
*
1129032 AAGGATGTCATAACTAAAATGCATGAAAGGATG-
131 AAGGATGACATAACTAAAATGCATGAAAGGATGC
* *
1129065 CAT---T--AAGGCATGAAAGGATGCATTAAGGCATGAAATGATGCCATAACTAAAATGCATGAA
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
* *
1129125 ATGATGCATTAATGAATGAAAGGATGCCATAACTAAAATGTATGAAATGATGCATTAAGGCATGA
66 ATGATGCATTAAGGAATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGCATGA
* *
1129190 AAAGATGCCATAACTAAAATGCATGAAAGGATGC
131 AAGGATGACATAACTAAAATGCATGAAAGGATGC
*
1129224 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAA
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
* *
1129289 AGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGCATGA
66 ATGATGCATTAAGGAATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGCATGA
1129354 AAGGATGACATAACTAAAATGCATGAAAGGATGC
131 AAGGATGACATAACTAAAATGCATGAAAGGATGC
1129388 ATTAAGGCAT
Statistics
Matches: 294, Mismatches: 21, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
156 49 0.17
158 92 0.31
159 3 0.01
161 3 0.01
162 1 0.00
164 146 0.50
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.22
Consensus pattern (164 bp):
CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
ATGATGCATTAAGGAATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGCATGA
AAGGATGACATAACTAAAATGCATGAAAGGATGC
Found at i:1129319 original size:210 final size:202
Alignment explanation
Indices: 1128904--1129499 Score: 801
Period size: 210 Copynumber: 2.9 Consensus size: 202
1128894 AAAATGAATT
* * * *
1128904 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATAAAAGGGTGCCATAACTAAAATGCGTG--
1 CATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
* * *
1128967 ATGATGCATTAAGGTATGAAAGGGTGCCATAACTAAAATGCATGAAAAGATG-CATTAAGGCATG
66 ATGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCCATTAAGGCATG
*
1129031 AAAGGATGTCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCATTAAGGCAT
131 AAAGGATGTCAT-A-T-AAAGGCATGAAAGGATGCATTAAGGCATGAAAGGATGCATTAAGGCAT
*
1129096 GAAATGATGC
193 GAAAGGATGC
* * *
1129106 CATAACTAAAATGCATGAAATGATGCATTAATGAATGAAAGGATGCCATAACTAAAATGTATGAA
1 CATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
* *
1129171 ATGATGCATTAAGGCATGAAAAGATGCCATAACTAAAATGCATGAAAGGATGCCATAACTAAAAT
66 ATGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCCAT---T--AAG
*
1129236 GCATGAAAGGATG-CAT-T-AAGGCATGAAAGGATGTCATAACTAAAATGCATGAAAGGATGCAT
126 GCATGAAAGGATGTCATATAAAGGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATGCAT
1129298 TAAGGCATGAAAGGATGC
185 TAAGGCATGAAAGGATGC
*
1129316 CATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGACATAACTAAAATGCATGAA
1 CATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
* *
1129381 AGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATACATGAAAGGATG-CATTAAGGCATG
66 ATGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCCATTAAGGCATG
* * *
1129445 AAAGGATGACATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGC
131 AAAGGATGTCAT-A-T-AAAGGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1129500 CATAATTAAA
Statistics
Matches: 348, Mismatches: 26, Indels: 38
0.84 0.06 0.09
Matches are distributed among these distances:
202 56 0.16
204 93 0.27
205 9 0.03
206 3 0.01
208 3 0.01
209 9 0.03
210 175 0.50
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (202 bp):
CATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
ATGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCCATTAAGGCATG
AAAGGATGTCATATAAAGGCATGAAAGGATGCATTAAGGCATGAAAGGATGCATTAAGGCATGAA
AGGATGC
Found at i:1129540 original size:20 final size:20
Alignment explanation
Indices: 1129006--1129543 Score: 185
Period size: 20 Copynumber: 23.6 Consensus size: 20
1128996 TAACTAAAAT
*
1129006 GCATGAAAAGATGCATTAAG
1 GCATGAAATGATGCATTAAG
* *
1129026 GCATGAAAGGATGTCATAACTAAAAT
1 GCATGAAATGATG-CAT---T--AAG
*
1129052 GCATGAAAGGATGCATTAAG
1 GCATGAAATGATGCATTAAG
*
1129072 GCATGAAAGGATGCATTAAG
1 GCATGAAATGATGCATTAAG
*
1129092 GCATGAAATGATGCCATAACTAAAAT
1 GCATGAAATGATG-CAT---T--AAG
*
1129118 GCATGAAATGATGCATTAAT
1 GCATGAAATGATGCATTAAG
* * *
1129138 GAATGAAAGGATGCCATAACTAAAAT
1 GCATGAAATGATG-CAT---T--AAG
*
1129164 GTATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
* *
1129184 GCATGAAAAGATGCCATAACTAAAAT
1 GCATGAAATGATG-CAT---T--AAG
* *
1129210 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAATGATG-CAT---T--AAG
*
1129236 GCATGAAAGGATGCATTAAG
1 GCATGAAATGATGCATTAAG
* *
1129256 GCATGAAAGGATGTCATAACTAAAAT
1 GCATGAAATGATG-CAT---T--AAG
*
1129282 GCATGAAAGGATGCATTAAG
1 GCATGAAATGATGCATTAAG
* *
1129302 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAATGATG-CAT---T--AAG
1129328 GCATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
* *
1129348 GCATGAAAGGATGACATAACTAAAAT
1 GCATGAAATGATG-CAT---T--AAG
*
1129374 GCATGAAAGGATGCATTAAG
1 GCATGAAATGATGCATTAAG
* *
1129394 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAATGATG-CAT---T--AAG
* *
1129420 ACATGAAAGGATGCATTAAG
1 GCATGAAATGATGCATTAAG
* *
1129440 GCATGAAAGGATGACATAACTAAAAT
1 GCATGAAATGATG-CAT---T--AAG
*
1129466 GCATGAAAGGATGCATTAAG
1 GCATGAAATGATGCATTAAG
*
1129486 GCATGAAATGATGCCATAATTAAAAT
1 GCATGAAATGATG-C---ATT--AAG
1129512 GCATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
*
1129532 GCCTGAAATGAT
1 GCATGAAATGAT
1129544 ACGATAACTA
Statistics
Matches: 425, Mismatches: 33, Indels: 120
0.74 0.06 0.21
Matches are distributed among these distances:
20 173 0.41
21 28 0.07
22 12 0.03
24 12 0.03
25 28 0.07
26 172 0.40
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
GCATGAAATGATGCATTAAG
Found at i:1138962 original size:24 final size:24
Alignment explanation
Indices: 1138930--1138984 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
1138920 GAAAATCCTC
1138930 AAGCTTCTT-TCCTTCTTCTCCATT
1 AAGCTTCTTAT-CTTCTTCTCCATT
1138954 AAGCTTCTTATCTTCTTCTCCATT
1 AAGCTTCTTATCTTCTTCTCCATT
1138978 AAGCTTC
1 AAGCTTC
1138985 ACATAATCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 29 0.97
25 1 0.03
ACGTcount: A:0.16, C:0.31, G:0.05, T:0.47
Consensus pattern (24 bp):
AAGCTTCTTATCTTCTTCTCCATT
Found at i:1149631 original size:17 final size:17
Alignment explanation
Indices: 1149599--1149632 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1149589 AAAATGTATG
*
1149599 AAATTATTTTAAAAAAT
1 AAATTATTTGAAAAAAT
*
1149616 AAATTATTTGATAAAAT
1 AAATTATTTGAAAAAAT
1149633 TAACAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
AAATTATTTGAAAAAAT
Found at i:1149844 original size:140 final size:140
Alignment explanation
Indices: 1149463--1149858 Score: 381
Period size: 146 Copynumber: 2.8 Consensus size: 140
1149453 AAAGATATAT
* * * * *
1149463 AAAACTAATATTATCTGATAAAGTTAACAGCAATTTATATATATAATCATTAAATTAAATTTTGT
1 AAAAATAA-ATTATTTGATAAAATTAACAACAATTTATATATATAATCATTAAATTAAATTTTTT
* * * * *
1149528 AATTTAAGTAATATTTTAAATATTTACTAATAATTTCAGATATATATATATATATTATTAAAAAA
65 AACTTAACTAATAATTTAAAAATTTATTAATAATTT---ATATATATATATATATTATT--AAAA
* *
1149593 TGTATGAAATTATTTTA
125 TGCA-GAAAATATTTTA
* **
1149610 AAAAATAAATTATTTGATAAAATTAACAATAATTTATATATATAATCATCGAATT-AATTTTTTA
1 AAAAATAAATTATTTGATAAAATTAACAACAATTTATATATATAATCATTAAATTAAATTTTTTA
* *
1149674 ACTTAACTAATAATTTTAAAATTTTAATTAATAATATTATATATATATATATA-TATT-AACT-C
66 ACTTAACTAATAA-TTTAAAAATTT-ATTAATAAT-TTATATATATATATATATTATTAAAATGC
1149736 A-AAAATA-TTTA
128 AGAAAATATTTTA
* * * *
1149747 AAAAACTTACATTGTTTGATAAATTTAACTAACAATTTTTATATATAATCATTAAATTAAAATTT
1 AAAAA--TAAATTATTTGATAAAATTAAC-AACAATTTATATATATAATCATTAAATT-AAATTT
* * ** * *
1149812 TTTAAGTTAATTAATAATTTAAAAAAATATTAATGATTTTTATATAT
62 TTTAACTTAACTAATAATTTAAAAATTTATTAATAATTTATATATAT
1149859 TTTAACTTAA
Statistics
Matches: 210, Mismatches: 31, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
137 9 0.04
138 5 0.02
139 28 0.13
140 33 0.16
141 11 0.05
142 20 0.10
144 4 0.02
145 33 0.16
146 50 0.24
147 15 0.07
148 2 0.01
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (140 bp):
AAAAATAAATTATTTGATAAAATTAACAACAATTTATATATATAATCATTAAATTAAATTTTTTA
ACTTAACTAATAATTTAAAAATTTATTAATAATTTATATATATATATATATTATTAAAATGCAGA
AAATATTTTA
Found at i:1151400 original size:22 final size:22
Alignment explanation
Indices: 1151370--1151417 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
1151360 TGGATGCATG
*
1151370 AGATGTTATGAAACATACTATT
1 AGATATTATGAAACATACTATT
1151392 AGATATTATGAAACATACTATT
1 AGATATTATGAAACATACTATT
1151414 AGAT
1 AGAT
1151418 GATCTGCTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.35
Consensus pattern (22 bp):
AGATATTATGAAACATACTATT
Found at i:1152412 original size:14 final size:14
Alignment explanation
Indices: 1152393--1152420 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1152383 GATGGACTAC
1152393 AACGTTAGTACTGT
1 AACGTTAGTACTGT
1152407 AACGTTAGTACTGT
1 AACGTTAGTACTGT
1152421 GGACTGCCAC
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:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
AACGTTAGTACTGT
Found at i:1155387 original size:13 final size:13
Alignment explanation
Indices: 1155369--1155393 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1155359 CTACTCCATG
1155369 TTTTTGCATTCGA
1 TTTTTGCATTCGA
1155382 TTTTTGCATTCG
1 TTTTTGCATTCG
1155394 GTACAGGTCT
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:0.12, C:0.16, G:0.16, T:0.56
Consensus pattern (13 bp):
TTTTTGCATTCGA
Found at i:1161709 original size:16 final size:16
Alignment explanation
Indices: 1161685--1161718 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1161675 TACTAACCAC
* *
1161685 TAATTGTTAACTTTTT
1 TAATAGTTAACATTTT
1161701 TAATAGTTAACATTTT
1 TAATAGTTAACATTTT
1161717 TA
1 TA
1161719 GCTGCTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (16 bp):
TAATAGTTAACATTTT
Found at i:1163637 original size:42 final size:42
Alignment explanation
Indices: 1163577--1163668 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
1163567 CCCGAAATCA
*
1163577 TGTGTTTGTTTCACGTAATTCGTTTTATGGAAAATGTTTTCC
1 TGTGTTTGTTTCACGTAATTCGTTTTACGGAAAATGTTTTCC
* * *
1163619 TGTGTTTGTTTCATGTAATTTGTTTTCCGGAAAATGTTTTCC
1 TGTGTTTGTTTCACGTAATTCGTTTTACGGAAAATGTTTTCC
*
1163661 AGTGTTTG
1 TGTGTTTG
1163669 GTTGGAGGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.17, C:0.11, G:0.21, T:0.51
Consensus pattern (42 bp):
TGTGTTTGTTTCACGTAATTCGTTTTACGGAAAATGTTTTCC
Found at i:1163917 original size:19 final size:19
Alignment explanation
Indices: 1163826--1163923 Score: 51
Period size: 19 Copynumber: 4.9 Consensus size: 19
1163816 ATTTTATGAA
1163826 TTTAATATTAATAAAATATT
1 TTTAAT-TTAATAAAATATT
1163846 TTAATATCATATTAATCAAAATA--
1 TT--TA--AT-TTAAT-AAAATATT
* *
1163869 -TTAA-TTATTAAATTATT
1 TTTAATTTAATAAAATATT
**
1163886 TATTAATAAAATAAAATATT
1 T-TTAATTTAATAAAATATT
*
1163906 TTTAATTTAATAATATAT
1 TTTAATTTAATAAAATAT
1163924 ACTAAATTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 21
0.66 0.10 0.24
Matches are distributed among these distances:
15 5 0.08
16 4 0.07
18 1 0.02
19 18 0.31
20 14 0.24
22 3 0.05
24 8 0.14
25 6 0.10
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAATTTAATAAAATATT
Found at i:1163992 original size:19 final size:19
Alignment explanation
Indices: 1163968--1164042 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 19
1163958 ATTTCATAGA
*
1163968 AATAATATTATTAATAATG
1 AATAATATTATTAATAATT
*
1163987 AATAATATTATTTACATATTT
1 AATAATATTA-TTA-ATAATT
* *
1164008 AATATTAATA-TAATAATCT
1 AATAATATTATTAATAAT-T
1164027 AATAATATT-TTAATAA
1 AATAATATTATTAATAA
1164043 AGATATTTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
18 4 0.09
19 26 0.58
20 3 0.07
21 12 0.27
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (19 bp):
AATAATATTATTAATAATT
Found at i:1164063 original size:23 final size:23
Alignment explanation
Indices: 1164037--1164081 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1164027 AATAATATTT
1164037 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1164060 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1164082 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1164208 original size:19 final size:20
Alignment explanation
Indices: 1164176--1164214 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1164166 TAATAAAATT
1164176 ATAAAAAAAATA-TTTAATA
1 ATAAAAAAAATATTTTAATA
* *
1164195 ATAAATAAATTATTTTAATA
1 ATAAAAAAAATATTTTAATA
1164215 TTTTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAAAAAAATATTTTAATA
Found at i:1164414 original size:14 final size:14
Alignment explanation
Indices: 1164380--1164420 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1164370 AAATGTAATT
*
1164380 CATTTTACGGAAAA
1 CATTTTCCGGAAAA
1164394 CATTTTCCGGAAAA
1 CATTTTCCGGAAAA
* *
1164408 CGTTTTCCAGAAA
1 CATTTTCCGGAAA
1164421 TGTAATTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (14 bp):
CATTTTCCGGAAAA
Found at i:1164457 original size:15 final size:15
Alignment explanation
Indices: 1164422--1164480 Score: 95
Period size: 14 Copynumber: 4.1 Consensus size: 15
1164412 TTCCAGAAAT
1164422 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
1164437 -TAATTCATTTTCCA
1 GTAATTCATTTTCCA
1164451 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
*
1164466 G-AATTCAATTTCCA
1 GTAATTCATTTTCCA
1164480 G
1 G
1164481 AAAACCAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
14 27 0.64
15 15 0.36
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:1164464 original size:29 final size:29
Alignment explanation
Indices: 1164422--1164480 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1164412 TTCCAGAAAT
* *
1164422 GTAATTCATTTTCCATAATTCATTTTCCA
1 GTAATTCATTTTCCAGAATTCAATTTCCA
1164451 GTAATTCATTTTCCAGAATTCAATTTCCA
1 GTAATTCATTTTCCAGAATTCAATTTCCA
1164480 G
1 G
1164481 AAAACCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAATTTCCA
Found at i:1165594 original size:46 final size:46
Alignment explanation
Indices: 1165522--1165618 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 46
1165512 CTGCTAACCC
* *
1165522 CTAACTGCTAACTTTTTTAACAGTTAACATTTCTAACTACTAATCA
1 CTAACTGCTAACTTTTCTAACAGTTAACATTTCAAACTACTAATCA
* * * *
1165568 CTAATTGCTAACTTTTCTAACTGTTAACATTTCAAACTGCTAATTA
1 CTAACTGCTAACTTTTCTAACAGTTAACATTTCAAACTACTAATCA
1165614 CTAAC
1 CTAAC
1165619 CCTTAACCTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.39
Consensus pattern (46 bp):
CTAACTGCTAACTTTTCTAACAGTTAACATTTCAAACTACTAATCA
Found at i:1165595 original size:16 final size:16
Alignment explanation
Indices: 1165522--1165610 Score: 67
Period size: 16 Copynumber: 5.7 Consensus size: 16
1165512 CTGCTAACCC
*
1165522 CTAACTGCTAACTTTT
1 CTAACTGCTAACATTT
* * *
1165538 TTAACAGTTAACATTT
1 CTAACTGCTAACATTT
*
1165554 CTAACTACTAATCA---
1 CTAACTGCTAA-CATTT
* *
1165568 CTAATTGCTAACTTTT
1 CTAACTGCTAACATTT
*
1165584 CTAACTGTTAACATTT
1 CTAACTGCTAACATTT
*
1165600 CAAACTGCTAA
1 CTAACTGCTAA
1165611 TTACTAACCC
Statistics
Matches: 53, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
13 1 0.02
14 9 0.17
16 41 0.77
17 2 0.04
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.39
Consensus pattern (16 bp):
CTAACTGCTAACATTT
Found at i:1165839 original size:14 final size:14
Alignment explanation
Indices: 1165820--1165855 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1165810 ACTTTATTTA
1165820 TTTAATTTCAGTCC
1 TTTAATTTCAGTCC
* *
1165834 TTTAATTTCATTGC
1 TTTAATTTCAGTCC
1165848 TTTAATTT
1 TTTAATTT
1165856 TCTATCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.58
Consensus pattern (14 bp):
TTTAATTTCAGTCC
Found at i:1167684 original size:24 final size:22
Alignment explanation
Indices: 1167652--1167696 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1167642 GAGATCATAA
*
1167652 CATGAATAAACCAAAAAGTTAAAC
1 CATGAAT-AA-CAAAAAGGTAAAC
*
1167676 CATGCATAACAAAAAGGTAAA
1 CATGAATAACAAAAAGGTAAA
1167697 ATAGCAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.58, C:0.16, G:0.11, T:0.16
Consensus pattern (22 bp):
CATGAATAACAAAAAGGTAAAC
Found at i:1168558 original size:19 final size:20
Alignment explanation
Indices: 1168521--1168564 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1168511 TGGTATTTTG
* *
1168521 TAATAATATTTATAATAATA
1 TAATAATACTAATAATAATA
*
1168541 -AATAATACTAATACTAATA
1 TAATAATACTAATAATAATA
1168560 TAATA
1 TAATA
1168565 TAATAATCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATAATACTAATAATAATA
Found at i:1169015 original size:91 final size:91
Alignment explanation
Indices: 1168860--1169585 Score: 1021
Period size: 91 Copynumber: 8.0 Consensus size: 91
1168850 GAAACAAGCT
* * *
1168860 AAGGTTGAACAAGTTCTTCTTATTATGAATTTATTCTCCCTCATCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
* *
1168925 GAACTCTCCATTAGAAATGTTGA-GCC
66 GAACTCTCCACTGGAAATGTTGATG-C
* *
1168951 AAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
*
1169016 GAACTATCCACTGGAAATGTTGA-GCC
66 GAACTCTCCACTGGAAATGTTGATG-C
* * *
1169042 AAGGTTGAACAAATTTTTCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
*
1169107 GAACTCTCCACTAGAAATGTTGA-GCC
66 GAACTCTCCACTGGAAATGTTGATG-C
* *
1169133 AAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTCATCGGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
* *
1169198 GAACTCCCCACTGTAAATGTTGATGC
66 GAACTCTCCACTGGAAATGTTGATGC
*
1169224 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGACGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
*
1169289 GAACTC-CCTGCTGGAAATGTTGATGC
66 GAACTCTCC-ACTGGAAATGTTGATGC
*
1169315 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
*
1169380 GAACTC-CTCGCTGGAAATGTTGATGC
66 GAACTCTC-CACTGGAAATGTTGATGC
* * ** *
1169406 ATGGTTGAACAAGTTCTACTCATTATGAACTTCTTCTCCCTTGTCGAATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
* * *
1169471 GAACTCCCCGCTGGAAATGTTGATGA
66 GAACTCTCCACTGGAAATGTTGATGC
* * * * * * * *
1169497 AAGATTCAACAGGTTCTACTCATTATGAACTTCTTCTCCCTCGTCAGATGAATTATTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
* **
1169562 GAACTCCCCGTTGGAAATGTTGAT
66 GAACTCTCCACTGGAAATGTTGAT
1169586 TGGTTTATCA
Statistics
Matches: 589, Mismatches: 42, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
90 2 0.00
91 584 0.99
92 3 0.01
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (91 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATGTTGATGC
Found at i:1172786 original size:23 final size:23
Alignment explanation
Indices: 1172756--1172830 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
1172746 TCTGATATAG
1172756 GCATCTGAGATGTATT-AAGGCTT
1 GCATCTGAGATGT-TTAAAGGCTT
1172779 GCATCTGAGATGTTTAAAGGCTT
1 GCATCTGAGATGTTTAAAGGCTT
1172802 GCATCTGAGATGTTTAAAGGCTT
1 GCATCTGAGATGTTTAAAGGCTT
1172825 GCATCT
1 GCATCT
1172831 AATCAATTCT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
22 2 0.04
23 49 0.96
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (23 bp):
GCATCTGAGATGTTTAAAGGCTT
Found at i:1176366 original size:65 final size:65
Alignment explanation
Indices: 1176262--1176525 Score: 312
Period size: 65 Copynumber: 4.1 Consensus size: 65
1176252 TTTCAGAGTG
1176262 ATGCACTGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATT
1 ATGCACTGATGCACC-ATCCATGCATCGATGCACTCA-GGAATAAATTGAAACATCGAATGCATT
1176325 TC
64 TC
1176327 ATGCACTGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATT
1 ATGCACTGATGCACC-ATCCATGCATCGATGCACTCA-GGAATAAATTGAAACATCGAATGCATT
1176390 TC
64 TC
* * **
1176392 ATGCACTGATGCA-CATACTATGCATCGATGCACTCA-GAGT-TTTATGAAAACATCGAATGCAT
1 ATGCACTGATGCACCAT-CCATGCATCGATGCACTCAGGAATAAAT-TG-AAACATCGAATGCAT
*
1176454 TTG
63 TTC
* **
1176457 ATGCA-TCGATGCACCATCCATGCATCGATGCACTCAGG-CTATTTTGAAACATCGAATGCATTT
1 ATGCACT-GATGCACCATCCATGCATCGATGCACTCAGGAATAAATTGAAACATCGAATGCATTT
*
1176520 T
65 C
1176521 ATGCA
1 ATGCA
1176526 TCGTTGCACT
Statistics
Matches: 182, Mismatches: 8, Indels: 19
0.87 0.04 0.09
Matches are distributed among these distances:
62 1 0.01
63 7 0.04
64 39 0.21
65 128 0.70
66 7 0.04
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (65 bp):
ATGCACTGATGCACCATCCATGCATCGATGCACTCAGGAATAAATTGAAACATCGAATGCATTTC
Found at i:1176550 original size:64 final size:64
Alignment explanation
Indices: 1176375--1176554 Score: 201
Period size: 65 Copynumber: 2.8 Consensus size: 64
1176365 GAATAAATTG
1176375 AACATCGAATGCATTTCATGCA-CTGATGCACATAC-TATGCATCGATGCACTCAGAGTTTTATG
1 AACATCGAATGCATTTCATGCATC-GATGCAC-T-CTTATGCATCGATGCACTCAGAGTTTTATG
1176438 AA
63 AA
* *
1176440 AACATCGAATGCATTTGATGCATCGATGCAC-CATCCATGCATCGATGCACTCAG-GCTATTT-T
1 AACATCGAATGCATTTCATGCATCGATGCACTC-T-TATGCATCGATGCACTCAGAG-T-TTTAT
1176502 G-A
62 GAA
* * *
1176504 AACATCGAATGCATTTTATGCATCGTTGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACTCTTA-TGCATCGATGCACT
1176555 AAGGGTCCAA
Statistics
Matches: 101, Mismatches: 6, Indels: 17
0.81 0.05 0.14
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 45 0.45
65 50 0.50
66 4 0.04
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTTATGCATCGATGCACTCAGAGTTTTATGAA
Found at i:1176550 original size:129 final size:130
Alignment explanation
Indices: 1176310--1176554 Score: 324
Period size: 129 Copynumber: 1.9 Consensus size: 130
1176300 GAATAAATTG
1176310 AACATCGAATGCATTTCATGCACTGATGCACCAATCCATGCATCGATGCACCATGGAATAAATTG
1 AACATCGAATGCATTTCATGCACTGATGCACCAATCCATGCATCGATGCACCATGGAATAAATTG
*
1176375 AACATCGAATGCATTTCATGCACTGATGCACATACTATGCATCGATGCACTCAGAGTTTTATGAA
66 AACATCGAATGCATTTCATGCACTGATGCACATACTATGCACCGATGCACTCAGAGTTTTATGAA
* * **
1176440 AACATCGAATGCATTTGATGCA-TCGATGCACC-ATCCATGCATCGATGCACTCA-GG-CTATTT
1 AACATCGAATGCATTTCATGCACT-GATGCACCAATCCATGCATCGATGCAC-CATGGAATAAAT
* *
1176501 TGAAACATCGAATGCATTTTATGCA-TCGTTGCAC-T-CTTAGTGCACCGATGCACT
64 TG-AACATCGAATGCATTTCATGCACT-GATGCACATAC-TA-TGCACCGATGCACT
1176555 AAGGGTCCAA
Statistics
Matches: 102, Mismatches: 7, Indels: 13
0.84 0.06 0.11
Matches are distributed among these distances:
127 1 0.01
128 9 0.09
129 61 0.60
130 31 0.30
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (130 bp):
AACATCGAATGCATTTCATGCACTGATGCACCAATCCATGCATCGATGCACCATGGAATAAATTG
AACATCGAATGCATTTCATGCACTGATGCACATACTATGCACCGATGCACTCAGAGTTTTATGAA
Found at i:1184007 original size:25 final size:25
Alignment explanation
Indices: 1183979--1184029 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
1183969 TAAAGAACCC
1183979 AAAATAAA-CTTAAACATACCATTAA
1 AAAATAAAGCTTAAACAT-CCATTAA
*
1184004 AAAATAAAGTTTAAACATCCATTAA
1 AAAATAAAGCTTAAACATCCATTAA
1184029 A
1 A
1184030 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (25 bp):
AAAATAAAGCTTAAACATCCATTAA
Found at i:1194252 original size:24 final size:24
Alignment explanation
Indices: 1194225--1194274 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1194215 TAAAGAACCC
1194225 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
1194249 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
1194273 AA
1 AA
1194275 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:1196488 original size:2 final size:2
Alignment explanation
Indices: 1196481--1196511 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1196471 CAGCTTAAGC
1196481 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1196512 TTAATCAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1197112 original size:45 final size:46
Alignment explanation
Indices: 1196997--1197120 Score: 164
Period size: 46 Copynumber: 2.7 Consensus size: 46
1196987 GAATAACTTG
* *
1196997 AACATCGAATGCATTTCATGCACCGATGCACTTAGAGTTTTATGAA
1 AACATCGAATGCATTTCATGCATCGATGCACTCAGAGTTTTATGAA
*
1197043 AACATCGAATGCATTTGATGCATCGATGCACTCAG-GCTATTT-TG-A
1 AACATCGAATGCATTTCATGCATCGATGCACTCAGAG-T-TTTATGAA
* *
1197088 AACATCGAATGCATTTTATTCATCGATGCACTC
1 AACATCGAATGCATTTCATGCATCGATGCACTC
1197121 TTAGTGCACC
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
45 33 0.46
46 35 0.49
47 3 0.04
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (46 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCAGAGTTTTATGAA
Found at i:1200053 original size:20 final size:20
Alignment explanation
Indices: 1200001--1200056 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
1199991 ATACCGGATG
* *
1200001 GGGTATCAATACCATAGTAT
1 GGGTATCGATACCATAGTAA
* *
1200021 GGTAGTATTGATACCATGGTAA
1 GG--GTATCGATACCATAGTAA
1200043 GGGTATCGATACCA
1 GGGTATCGATACCA
1200057 GGCAACATCA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 13 0.45
22 16 0.55
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAA
Found at i:1200087 original size:94 final size:95
Alignment explanation
Indices: 1199926--1200149 Score: 256
Period size: 94 Copynumber: 2.4 Consensus size: 95
1199916 GATACCAAAG
* ** *
1199926 TGGTAGTATCGATACCATGGTAAGTGTATCGATACCAGGAATCATTGAATATAAAATTGGTATCG
1 TGGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAATCATCAAACATAAAATTGGTATCG
* *
1199991 ATACCG-GATGGGGTATCAATACCATAGTA
66 ATACCGAAAGGGGGTATCAATACCATAGTA
* * *
1200020 TGGTAGTATTGATACCATGGTAAGGGTATCGATACCAGGCAA-CATCAAACCTAAAATTTGTATC
1 TGGTAGTATCGATACCATGGTAAGGGTATCGATACCAGG-AATCATCAAACATAAAATTGGTATC
* **
1200084 GATACTGAAAGGGGGTATCGGTACCATAGTA
65 GATACCGAAAGGGGGTATCAATACCATAGTA
* * * * *
1200115 TAGAAGTATCGGTACCAGGGT-AGTAGTATCGATAC
1 TGGTAGTATCGATACCATGGTAAG-GGTATCGATAC
1200150 TATAGAGCCA
Statistics
Matches: 109, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
94 62 0.57
95 47 0.43
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (95 bp):
TGGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAATCATCAAACATAAAATTGGTATCG
ATACCGAAAGGGGGTATCAATACCATAGTA
Found at i:1200537 original size:59 final size:59
Alignment explanation
Indices: 1200468--1200762 Score: 473
Period size: 59 Copynumber: 5.0 Consensus size: 59
1200458 GATTACAAAA
* ** *
1200468 AGGGCACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * * *
1200527 AAGGAACTTCGTGTGCTAACATGAGAAGGAATTCACACTAAGTGTATGAATTTACATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
*
1200586 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTATGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* *
1200645 AGGGCATTTCGTGAGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* *
1200704 AGGGCACTTCGTGTGCTAACATGGGAAGGAATTCATACTAAGTGTATGAATTTTCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1200763 GGAAATATTT
Statistics
Matches: 216, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 216 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (59 bp):
AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
Found at i:1201247 original size:68 final size:68
Alignment explanation
Indices: 1201113--1201247 Score: 153
Period size: 68 Copynumber: 2.0 Consensus size: 68
1201103 AGATTAAAGG
** * * * *
1201113 CCTAACTATGCATTTGACAGGAAGGTATCAATTATGCCAGTTAGATGAAAGGCCAAGTGCCTTTG
1 CCTAACTATGCAAATGACAGAAAGGTATCAATTATGCCAGTTAGATGAAAGGCCAAATACCGTTG
1201178 AGA
66 AGA
* * * * * **
1201181 CCTAACTGTGCAAATGACAGAAAGGTGTCATTTATTCCAGTTAGATGAACGGTTAAATACCGTTG
1 CCTAACTATGCAAATGACAGAAAGGTATCAATTATGCCAGTTAGATGAAAGGCCAAATACCGTTG
1201246 AG
66 AG
1201248 TAAAAGAATA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
68 54 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (68 bp):
CCTAACTATGCAAATGACAGAAAGGTATCAATTATGCCAGTTAGATGAAAGGCCAAATACCGTTG
AGA
Found at i:1201318 original size:81 final size:81
Alignment explanation
Indices: 1201183--1201340 Score: 244
Period size: 81 Copynumber: 2.0 Consensus size: 81
1201173 CTTTGAGACC
* * * * *
1201183 TAACTGTGCAAATGACAGAAAGGTGTCATTTATTCCAGTTAGATGAACGGTTAAATACCGTTGAG
1 TAACTGTGCAAATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAACACCGTTGAA
1201248 TAAAAGAATAATGGCA
66 TAAAAGAATAATGGCA
* * *
1201264 TAACTGTGCAATTGACTGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAACACTGTTGAA
1 TAACTGTGCAAATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAACACCGTTGAA
1201329 TAAAAGAATAAT
66 TAAAAGAATAAT
1201341 AGATTAGTTG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 69 1.00
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (81 bp):
TAACTGTGCAAATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAACACCGTTGAA
TAAAAGAATAATGGCA
Found at i:1201697 original size:28 final size:28
Alignment explanation
Indices: 1201654--1201719 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
1201644 CATACTAGAA
*
1201654 TTGGTTATGAGAATAAAATGGCCAAGGT
1 TTGGTTATGAGAATAAAATGACCAAGGT
1201682 GTT-GTTATGAGAATAAAATGACCAAGGT
1 -TTGGTTATGAGAATAAAATGACCAAGGT
1201710 TTGGTTATGA
1 TTGGTTATGA
1201720 TACGAAGGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (28 bp):
TTGGTTATGAGAATAAAATGACCAAGGT
Found at i:1205167 original size:94 final size:95
Alignment explanation
Indices: 1205036--1205261 Score: 289
Period size: 94 Copynumber: 2.4 Consensus size: 95
1205026 AATTCAATCA
* * * *
1205036 GTATCGATATCAAAG-A-GGTAATATCGATACCATGGTAAGGGTATAGATACCAGG-AATCATTG
1 GTATCGATACCATAGCATGGTAGTATCGATACCATGGTAAGGGTATAGATACCAGGCAA-CATCG
* *
1205098 AATCTAAAATTGGCATCGATACCGAAA-GGG
65 AACCTAAAATTGGCATCGATACCAAAAGGGG
* *
1205128 GTATCGGTACCATAGCATGGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGCAACATCGA
1 GTATCGATACCATAGCATGGTAGTATCGATACCATGGTAAGGGTATAGATACCAGGCAACATCGA
* *
1205193 ACCTAAAATTTGTATCGATACCAAAAGGGG
66 ACCTAAAATTGGCATCGATACCAAAAGGGG
* * * *
1205223 GTATCGATACCATAGCATAGAAGTATCGGTACCAAGGTA
1 GTATCGATACCATAGCATGGTAGTATCGATACCATGGTA
1205262 GTAGTATTGA
Statistics
Matches: 115, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
92 12 0.10
93 1 0.01
94 63 0.55
95 39 0.34
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (95 bp):
GTATCGATACCATAGCATGGTAGTATCGATACCATGGTAAGGGTATAGATACCAGGCAACATCGA
ACCTAAAATTGGCATCGATACCAAAAGGGG
Found at i:1205952 original size:59 final size:59
Alignment explanation
Indices: 1205600--1205945 Score: 480
Period size: 59 Copynumber: 5.9 Consensus size: 59
1205590 ACAAAAAGGA
* * ** * *
1205600 CACTTCATGTGCTAAAATGTTAAGAAATTCATACTAAGTATATGAATTTCCATATAGGG
1 CACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGG
1205659 CACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGAGG
1 CACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG-GG
* *
1205719 -ACTTCATGTGCTAACATGAGAAGGAATTCAAACTAAGTGTATGAATTTCCATATAGGG
1 CACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGG
1205777 CACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGG
1 CACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGG
* * * *
1205836 CACTTCGTGTGCTAACATGGGAAGGAATTCATACTATGTGTATGAATTTCCAGATGGGG
1 CACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGG
* * * * * * * *
1205895 TACCTT-GTGTGCTAAAATGATAAGAAATTCATCCTTAGTCTATGATTTTCC
1 CA-CTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCC
1205946 GTATGGGAAA
Statistics
Matches: 260, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
58 2 0.01
59 253 0.97
60 5 0.02
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (59 bp):
CACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGG
Found at i:1206390 original size:24 final size:24
Alignment explanation
Indices: 1206361--1206430 Score: 122
Period size: 24 Copynumber: 2.9 Consensus size: 24
1206351 CATAATAGGA
1206361 ATGAAAGGATGCCATAATTAAGAC
1 ATGAAAGGATGCCATAATTAAGAC
1206385 ATGAAAGGATGCCATAATTAAGAC
1 ATGAAAGGATGCCATAATTAAGAC
*
1206409 ATTAAAGGATGCCATAAATTAA
1 ATGAAAGGATGCCAT-AATTAA
1206431 ATGTATAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
24 38 0.86
25 6 0.14
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (24 bp):
ATGAAAGGATGCCATAATTAAGAC
Found at i:1207067 original size:2 final size:2
Alignment explanation
Indices: 1207060--1207170 Score: 222
Period size: 2 Copynumber: 55.5 Consensus size: 2
1207050 AAATAAACGT
1207060 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
1207102 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
1207144 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1207171 TTACTTTTAT
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 109 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1207688 original size:3 final size:3
Alignment explanation
Indices: 1207671--1207721 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
1207661 AGGTATTTTG
* *
1207671 TAA TAA TAT TTA TAA TAAA TAA TAA TAA TAA TAA TAA T-A TAA T-A
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1207715 TAA TAA T
1 TAA TAA T
1207722 TTGAAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1207699 original size:22 final size:22
Alignment explanation
Indices: 1207672--1207721 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1207662 GGTATTTTGT
* *
1207672 AATAATATTTATAATA-AATAAT
1 AATAATAATAATAATATAAT-AT
1207694 AATAATAATAATAATATAATAT
1 AATAATAATAATAATATAATAT
1207716 AATAAT
1 AATAAT
1207722 TTGAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAATAATAATAATATAATAT
Found at i:1207717 original size:19 final size:19
Alignment explanation
Indices: 1207671--1207721 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
1207661 AGGTATTTTG
* *
1207671 TAATAATATTTATAATAAA
1 TAATAATAATAATAATAAA
1207690 TAATAATAATAATAATAATA
1 TAATAATAATAATAATAA-A
1207710 TAAT-ATAATAAT
1 TAATAATAATAAT
1207722 TTGAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 24 0.83
20 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATAATAATAATAATAAA
Found at i:1209797 original size:17 final size:19
Alignment explanation
Indices: 1209775--1209818 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1209765 TAAAACATTG
1209775 AATGCACT-TGA-TGCACC
1 AATGCACTCTGAGTGCACC
*
1209792 AATGCACTCTTAGTGCACC
1 AATGCACTCTGAGTGCACC
*
1209811 GATGCACT
1 AATGCACT
1209819 AAGGATCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 2 0.09
19 13 0.57
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (19 bp):
AATGCACTCTGAGTGCACC
Found at i:1217273 original size:21 final size:21
Alignment explanation
Indices: 1217231--1217274 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1217221 ACTCCGGGAG
* *
1217231 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
1217252 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
1217273 CT
1 CT
1217275 CCTTCTCCGG
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:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:1217677 original size:15 final size:15
Alignment explanation
Indices: 1217659--1217693 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1217649 GTTGCCTTTC
*
1217659 TTTGATTGTTGGATA
1 TTTGATTGATGGATA
*
1217674 TTTGTTTGATGGATA
1 TTTGATTGATGGATA
1217689 TTTGA
1 TTTGA
1217694 ACTTTTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (15 bp):
TTTGATTGATGGATA
Found at i:1218411 original size:19 final size:19
Alignment explanation
Indices: 1218387--1218439 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1218377 GAATGCATGT
*
1218387 CATGCATCGATGTA-CATAC
1 CATGCATCGATGCACCAT-C
1218406 CATGCAAT-GATGCACCATC
1 CATGC-ATCGATGCACCATC
1218425 CATGCATCGATGCAC
1 CATGCATCGATGCAC
1218440 TCTGGCTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.07
19 23 0.77
20 5 0.17
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (19 bp):
CATGCATCGATGCACCATC
Found at i:1224755 original size:24 final size:24
Alignment explanation
Indices: 1224710--1224761 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1224700 CATTAATATT
* *
1224710 TAAATAAACACTTAATAATTTACA
1 TAAATAAAAAATTAATAATTTACA
1224734 TAAATAAAAAATT-ATAAGTTTACA
1 TAAATAAAAAATTAATAA-TTTACA
1224758 -AAAT
1 TAAAT
1224762 CGATAAGAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAATAAAAAATTAATAATTTACA
Found at i:1225190 original size:21 final size:21
Alignment explanation
Indices: 1225160--1225211 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
1225150 CACCACAACT
1225160 CACATAATTT-ACACCGAAGTG-C
1 CACAT-ATTTGAC-CCGAA-TGAC
*
1225182 CACATATTTGTCCCGAATGAC
1 CACATATTTGACCCGAATGAC
1225203 CACATATTT
1 CACATATTT
1225212 TTGTCCCGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.07
21 19 0.70
22 6 0.22
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.29
Consensus pattern (21 bp):
CACATATTTGACCCGAATGAC
Found at i:1225218 original size:23 final size:23
Alignment explanation
Indices: 1225181--1225254 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
1225171 CACCGAAGTG
*
1225181 CCACATA--TTTGTCCCGAATGA
1 CCACATATTTTTGTCCCGAAAGA
*
1225202 CCACATATTTTTGTCCCGAAAAA
1 CCACATATTTTTGTCCCGAAAGA
*
1225225 TCACATATTTTTGTCCCGAAAGA
1 CCACATATTTTTGTCCCGAAAGA
1225248 CCACATA
1 CCACATA
1225255 GAACCCTCGA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.15
23 39 0.85
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (23 bp):
CCACATATTTTTGTCCCGAAAGA
Found at i:1227976 original size:45 final size:45
Alignment explanation
Indices: 1227924--1228160 Score: 289
Period size: 45 Copynumber: 5.3 Consensus size: 45
1227914 AATACATCAT
* ** * *
1227924 TATGCATTTTAAACTCTAACATA-TTTTCTATTGATAATGCACCTA
1 TATGCA-TTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCCA
* * *
1227969 TATGCATTTCAACTATAGTATACTTTTATGTTGATAATGTACCCA
1 TATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCCA
* * * * *
1228014 TATACATCTCAAC-CATAGTATACTTTTATGTTGATAATGTACCAA
1 TATGCATTTCAACTC-TAGTATACTTTTCTGTTGATAATGCACCCA
* * *
1228059 TATACATTTCAACTCTAGTATAATTTTCTATTGATAATGCACCCA
1 TATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCCA
*
1228104 TATGCATTTCAACTCTAGTATATTTTTCTGTTGATAATGCACCCA
1 TATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCCA
1228149 TATGCATTTCAA
1 TATGCATTTCAA
1228161 TTTGGCATCC
Statistics
Matches: 168, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
44 12 0.07
45 155 0.92
46 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (45 bp):
TATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCCA
Found at i:1228733 original size:22 final size:20
Alignment explanation
Indices: 1228691--1228750 Score: 93
Period size: 22 Copynumber: 2.9 Consensus size: 20
1228681 TGGCCCTTCA
*
1228691 GTATCGATACCCCCACTATG
1 GTATCGATACCCCTACTATG
1228711 GTATCGATACTACCCTACTATG
1 GTATCGATAC--CCCTACTATG
1228733 GTATCGATACCCCTACTA
1 GTATCGATACCCCTACTA
1228751 GTATCAATAC
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 18 0.49
22 19 0.51
ACGTcount: A:0.27, C:0.32, G:0.13, T:0.28
Consensus pattern (20 bp):
GTATCGATACCCCTACTATG
Found at i:1228835 original size:22 final size:22
Alignment explanation
Indices: 1228789--1228844 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
1228779 GGCCCAGTAT
*
1228789 CGATACCCT-TACCATAGGTAT
1 CGATACCCTATACCATAGGTAC
*
1228810 CGATACCACTATACTAT-GGTAC
1 CGATACC-CTATACCATAGGTAC
1228832 CGATACCCCTATA
1 CGATA-CCCTATA
1228845 AGGTATCGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 7 0.23
22 16 0.53
23 7 0.23
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.27
Consensus pattern (22 bp):
CGATACCCTATACCATAGGTAC
Found at i:1228836 original size:95 final size:93
Alignment explanation
Indices: 1228689--1228929 Score: 281
Period size: 95 Copynumber: 2.6 Consensus size: 93
1228679 TCTGGCCCTT
* * * * *
1228689 CAGTATCGATACCCCCACTATGGTATCGATACTACCCTACTATGGTATCGATACCCCTACT-A-G
1 CAGTATCGATACCCTCACCATGGTATCGATACCA-CTTACTATGGTACCGATACCCCTA-TAAGG
*
1228752 TATCAATACCAAAATTAGATTCGATGTGGCC
64 TATCAATA-CAAAATTAGATTCGATGTGACC
*
1228783 CAGTATCGATACCCTTACCATAGGTATCGATACCACTATACTATGGTACCGATACCCCTATAAGG
1 CAGTATCGATACCCTCACCAT-GGTATCGATACCACT-TACTATGGTACCGATACCCCTATAAGG
* * *
1228848 TATCGATACAAAATTAGGTTCGATGTTACC
64 TATCAATACAAAATTAGATTCGATGTGACC
* * * *
1228878 CAATATAGATACCCTCACCATGCTATCGATACCACTTCATTA-GGTACCGATA
1 CAGTATCGATACCCTCACCATGGTATCGATACCACTT-ACTATGGTACCGATA
1228930 ATGATTAAAT
Statistics
Matches: 127, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
93 11 0.09
94 37 0.29
95 71 0.56
96 8 0.06
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (93 bp):
CAGTATCGATACCCTCACCATGGTATCGATACCACTTACTATGGTACCGATACCCCTATAAGGTA
TCAATACAAAATTAGATTCGATGTGACC
Found at i:1234856 original size:45 final size:45
Alignment explanation
Indices: 1234594--1234870 Score: 290
Period size: 45 Copynumber: 6.2 Consensus size: 45
1234584 AATACATCAT
* *
1234594 TATGCATTTTAAACTCTAACATA-TTTTCTGTTGATAATGCACCCA
1 TATGCA-TTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
* ** * * * *
1234639 TATGCATTTCAACTATAATATACTTTTATTTTGATAATGTACCTA
1 TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
* * * * *
1234684 TATACGTTTCAAC-CATAGTATATTTTTCTGTTGATAATGTACCCA
1 TATGCATTTCAACTC-TAGCATACTTTTCTGTTGATAATGCACCCA
*
1234729 TATACATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
1 TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
* * *
1234774 TATGCATTTCAAATCTAGTATACTTTTCTGTTGATAATGCACACA
1 TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
* * *** *
1234819 TATGCATTTCAACTCTGGCAT-CCTTTCATGCCCATAATGCACCAA
1 TATGCATTTCAACTCTAGCATACTTTTC-TGTTGATAATGCACCCA
1234864 TATGCAT
1 TATGCAT
1234871 AATTCTTTTA
Statistics
Matches: 196, Mismatches: 32, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
44 18 0.09
45 177 0.90
46 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.40
Consensus pattern (45 bp):
TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
Found at i:1235397 original size:22 final size:20
Alignment explanation
Indices: 1235359--1235451 Score: 100
Period size: 22 Copynumber: 4.5 Consensus size: 20
1235349 TGTCCCTTCA
1235359 GTATCGATACCCCTACTATG
1 GTATCGATACCCCTACTATG
1235379 GTATCGATACTACCCTACTATG
1 GTATCGATAC--CCCTACTATG
* * *
1235401 ATATCTATATTACCCTACTATG
1 GTATCGATA--CCCCTACTATG
1235423 GTATCGATACCCCTACT-T-
1 GTATCGATACCCCTACTATG
*
1235441 GTATCAATACC
1 GTATCGATACC
1235452 AAAATTAGAT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
18 10 0.16
19 1 0.02
20 17 0.27
22 34 0.55
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (20 bp):
GTATCGATACCCCTACTATG
Found at i:1235530 original size:95 final size:94
Alignment explanation
Indices: 1235416--1235599 Score: 257
Period size: 95 Copynumber: 1.9 Consensus size: 94
1235406 TATATTACCC
*
1235416 TACTATGGTATCGATACCCCTACT-T-GTATCAATACCAAAATTAGATTCGATGTGGCCCAGTAT
1 TACTATGGTATCGATACCCCTA-TATGGTATCAATACCAAAATTAGATTCGATGTGACCC-GTAT
*
1235479 CGATACCCTTACCATAGGTATCGATACCACTA
64 CGATACCCTCACCAT-GGTATCGATACCACTA
* * * *
1235511 TACTATGGTA-CATATACCCCTATATGGTATCGATACCAAAATTAGGTTCGATGTTACCCGTATC
1 TACTATGGTATC-GATACCCCTATATGGTATCAATACCAAAATTAGATTCGATGTGACCCGTATC
1235575 GATACCCTCACCATGGTATCGATAC
65 GATACCCTCACCATGGTATCGATAC
1235600 TACTTCATTA
Statistics
Matches: 80, Mismatches: 6, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
94 13 0.16
95 38 0.47
96 29 0.36
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (94 bp):
TACTATGGTATCGATACCCCTATATGGTATCAATACCAAAATTAGATTCGATGTGACCCGTATCG
ATACCCTCACCATGGTATCGATACCACTA
Found at i:1240785 original size:23 final size:22
Alignment explanation
Indices: 1240745--1240820 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 22
1240735 CACCGATGTG
*
1240745 CCACATAG--TTGTCCCGAAGGA
1 CCACATAGTTTTGT-CCGAAAGA
1240766 CCACATAGTTTTGTCTCGAAAGA
1 CCACATAGTTTTGTC-CGAAAGA
* * *
1240789 CCATATTAGTTTTATCCTGAATGA
1 CCACA-TAGTTTTGTCC-GAAAGA
1240813 CCACATAG
1 CCACATAG
1240821 AACCCTCGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
21 8 0.18
22 1 0.02
23 18 0.40
24 18 0.40
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (22 bp):
CCACATAGTTTTGTCCGAAAGA
Found at i:1244210 original size:153 final size:155
Alignment explanation
Indices: 1243908--1244218 Score: 608
Period size: 153 Copynumber: 2.0 Consensus size: 155
1243898 CCTCATAGCG
1243908 TTGATGATTTCAAGAATATAGATAATGGGTCCATTTTCAAAGTTAACGGTCAGCGTCTGAAGGCT
1 TTGATGATTTCAAGAATATAGATAATGGGTCCATTTTCAAAGTTAACGGTCAGCGTCTGAAGGCT
1243973 TATCACAGAGCTCCGCCCTTACGTGACAAATCGAAACTCTTCTTGCAAGATACCGGAATCTGCTA
66 TATCACAGAGCTCCGCCCTTACGTGACAAATCGAAACTCTTCTTGCAAGATACCGGAATCTGCTA
1244038 AGCATTTTTAAGATGCCTTTACATT
131 AGCATTTTTAAGATGCCTTTACATT
1244063 TTGATGATTTC-AGAATATAGAT-ATGGGTCCATTTTCAAAGTTAACGGTCAGCGTCTGAAGGCT
1 TTGATGATTTCAAGAATATAGATAATGGGTCCATTTTCAAAGTTAACGGTCAGCGTCTGAAGGCT
1244126 TATCACAGAGCTCCGCCCTTACGTGACAAATCGAAACTCTTCTTGCAAGATACCGGAATCTGCTA
66 TATCACAGAGCTCCGCCCTTACGTGACAAATCGAAACTCTTCTTGCAAGATACCGGAATCTGCTA
1244191 AGCATTTTTAAGATGCCTTTACATT
131 AGCATTTTTAAGATGCCTTTACATT
1244216 TTG
1 TTG
1244219 GATTTACTCC
Statistics
Matches: 156, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
153 134 0.86
154 11 0.07
155 11 0.07
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (155 bp):
TTGATGATTTCAAGAATATAGATAATGGGTCCATTTTCAAAGTTAACGGTCAGCGTCTGAAGGCT
TATCACAGAGCTCCGCCCTTACGTGACAAATCGAAACTCTTCTTGCAAGATACCGGAATCTGCTA
AGCATTTTTAAGATGCCTTTACATT
Found at i:1246757 original size:20 final size:20
Alignment explanation
Indices: 1246720--1246758 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1246710 AGATCTCATA
*
1246720 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
* *
1246740 TAGGAGCATCTAGTTGCAT
1 TAGGAGCATATAGATGCAT
1246759 ATGGTGGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1247107 original size:25 final size:27
Alignment explanation
Indices: 1247066--1247126 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 27
1247056 ACGCCTAGCT
1247066 ACAAGCTGCCCAGGAGGGAACCAC-GCC
1 ACAA-CTGCCCAGGAGGGAACCACTGCC
*
1247093 -CAACTGCCCTA-GAGGGGACCACTGCC
1 ACAACTGCCC-AGGAGGGAACCACTGCC
1247119 ACAACTGC
1 ACAACTGC
1247127 TGACCCCCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 16 0.53
26 7 0.23
27 7 0.23
ACGTcount: A:0.28, C:0.38, G:0.26, T:0.08
Consensus pattern (27 bp):
ACAACTGCCCAGGAGGGAACCACTGCC
Found at i:1251549 original size:139 final size:137
Alignment explanation
Indices: 1251240--1251704 Score: 610
Period size: 139 Copynumber: 3.3 Consensus size: 137
1251230 CTCAGACAAT
* * ** * * *
1251240 TAGACTTCCTCATCACGAAGAAACAATGTCATCCACATACCAGGTCTCCTCAATGTGAAGGAGCA
1 TAGACTTCCTCATCACGAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGTGAAAGAGCA
* * *
1251305 ATGTCATCCTCATACAATCAGACTTCCTCA-ATGCGAAGGAACCGTGTTTGTCTCCAAATTATCC
66 GTGTCATCCTCAGAAAATCAGACTTCCTCACAT--GAAGGAACCGTG-TTGTCTCCAAATTATCC
1251369 CTAAAGATGGC
128 CTAAAGA-GGC
* *
1251380 TAGACTTCCTCATCACGAAGGAACAATGTCGTCCACCGACTAGATCTCATCAACGTGAAAGAGCA
1 TAGACTTCCTCATCACGAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGTGAAAGAGCA
* * *
1251445 GTGTCATCCTCAGAAAACCAGACTTCCTCATCATGAAGGAACTGTGTTGCCTCCAAATTATCCCT
66 GTGTCATCCTCAGAAAATCAGACTTCCTCA-CATGAAGGAACCGTGTTGTCTCCAAATTATCCCT
1251510 AAAGACGGC
130 AAAGA-GGC
* * * * *
1251519 TAGACATCCTCATCATGAAGGAACAATGTCGTTCACCGACCAGGTCTCCTCAACG-CAAAGAAGC
1 TAGACTTCCTCATCACGAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGTGAAAG-AGC
* * *
1251583 AGTGTCATCCTCAGATAATTAGACTTCCTCAACGTGAAGGAACCGTGTTGTCTCCAAATTATCCC
65 AGTGTCATCCTCAGAAAATCAGACTTCCTC-ACATGAAGGAACCGTGTTGTCTCCAAATTATCCC
1251648 TAAAGGAGGC
129 TAAA-GAGGC
* *
1251658 TAGACGTCCTCATCACGAAGGAACAATGTCGTCCACCGGCCAGATCT
1 TAGACTTCCTCATCACGAAGGAACAATGTCGTCCACCGACCAGATCT
1251705 TTTTAACATG
Statistics
Matches: 286, Mismatches: 34, Indels: 11
0.86 0.10 0.03
Matches are distributed among these distances:
138 4 0.01
139 184 0.64
140 96 0.34
142 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (137 bp):
TAGACTTCCTCATCACGAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGTGAAAGAGCA
GTGTCATCCTCAGAAAATCAGACTTCCTCACATGAAGGAACCGTGTTGTCTCCAAATTATCCCTA
AAGAGGC
Found at i:1253400 original size:16 final size:16
Alignment explanation
Indices: 1253375--1253456 Score: 78
Period size: 16 Copynumber: 5.2 Consensus size: 16
1253365 CTGCTAACCA
*
1253375 CTAACCGCTAACTTTT
1 CTAACAGCTAACTTTT
* *
1253391 TTAACAGCTAACATTT
1 CTAACAGCTAACTTTT
* **
1253407 CAAACAGCTAA--TCA
1 CTAACAGCTAACTTTT
*
1253421 CTAACCGCTAACTTTT
1 CTAACAGCTAACTTTT
*
1253437 CTAACAGCTAACCTTT
1 CTAACAGCTAACTTTT
1253453 CTAA
1 CTAA
1253457 TTGCTAATTA
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
14 10 0.20
16 41 0.80
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (16 bp):
CTAACAGCTAACTTTT
Found at i:1253434 original size:46 final size:46
Alignment explanation
Indices: 1253367--1253483 Score: 162
Period size: 46 Copynumber: 2.5 Consensus size: 46
1253357 TTCAGACTCT
*
1253367 GCTAACCACTAACCGCTAACTTTTTTAACAGCTAACATTTCAAACA
1 GCTAATCACTAACCGCTAACTTTTTTAACAGCTAACATTTCAAACA
* * * **
1253413 GCTAATCACTAACCGCTAACTTTTCTAACAGCTAACCTTTCTAATT
1 GCTAATCACTAACCGCTAACTTTTTTAACAGCTAACATTTCAAACA
* *
1253459 GCTAATTACTAACCGCTAACCTTTT
1 GCTAATCACTAACCGCTAACTTTTT
1253484 ATTTATTTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.32
Consensus pattern (46 bp):
GCTAATCACTAACCGCTAACTTTTTTAACAGCTAACATTTCAAACA
Found at i:1253462 original size:16 final size:16
Alignment explanation
Indices: 1253375--1253482 Score: 71
Period size: 16 Copynumber: 7.0 Consensus size: 16
1253365 CTGCTAACCA
* *
1253375 CTAACCGCTAACTTTT
1 CTAACAGCTAACCTTT
* *
1253391 TTAACAGCTAACATTT
1 CTAACAGCTAACCTTT
* **
1253407 CAAACAGCTAA--TCA
1 CTAACAGCTAACCTTT
* *
1253421 CTAACCGCTAACTTTT
1 CTAACAGCTAACCTTT
1253437 CTAACAGCTAACCTTT
1 CTAACAGCTAACCTTT
** *
1253453 CTAATTGCTAA--TTA
1 CTAACAGCTAACCTTT
*
1253467 CTAACCGCTAACCTTT
1 CTAACAGCTAACCTTT
1253483 TATTTATTTA
Statistics
Matches: 69, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
14 21 0.30
16 48 0.70
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.33
Consensus pattern (16 bp):
CTAACAGCTAACCTTT
Found at i:1253671 original size:14 final size:15
Alignment explanation
Indices: 1253632--1253672 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
1253622 TTTTTTGTTA
1253632 TTTAATTTCATGCACT
1 TTTAATTT-ATGCACT
1253648 TTTAAATTTATGC-CT
1 TTT-AATTTATGCACT
1253663 TTTAATTTAT
1 TTTAATTTAT
1253673 TTATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.29
15 5 0.21
16 7 0.29
17 5 0.21
ACGTcount: A:0.27, C:0.12, G:0.05, T:0.56
Consensus pattern (15 bp):
TTTAATTTATGCACT
Found at i:1253695 original size:14 final size:14
Alignment explanation
Indices: 1253676--1253711 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1253666 AATTTATTTA
1253676 TTTAATTTCAGTCC
1 TTTAATTTCAGTCC
* *
1253690 TTTAATTTCATTGC
1 TTTAATTTCAGTCC
1253704 TTTAATTT
1 TTTAATTT
1253712 TCTGTCTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.58
Consensus pattern (14 bp):
TTTAATTTCAGTCC
Found at i:1254738 original size:18 final size:18
Alignment explanation
Indices: 1254710--1254755 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
1254700 TAATAAAGTC
1254710 ATAATTG-TTTTTAAAAT
1 ATAATTGTTTTTTAAAAT
1254727 ATAATTGTTTTTTAAAAT
1 ATAATTGTTTTTTAAAAT
1254745 ATAATTGTTTT
1 ATAATTGTTTT
1254756 AAAAAGATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (18 bp):
ATAATTGTTTTTTAAAAT
Found at i:1262809 original size:16 final size:16
Alignment explanation
Indices: 1262778--1262820 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1262768 AAATGACTTG
*
1262778 AACTCGAAAATGACCCA
1 AACTC-AAAATAACCCA
* *
1262795 AACTCCAAATAACCCT
1 AACTCAAAATAACCCA
1262811 AACTCAAAAT
1 AACTCAAAAT
1262821 CATCTAGACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.49, C:0.30, G:0.05, T:0.16
Consensus pattern (16 bp):
AACTCAAAATAACCCA
Found at i:1266756 original size:37 final size:37
Alignment explanation
Indices: 1266715--1266789 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
1266705 TTTTAAAAAG
1266715 ATAAATTTTTAAAATATAAAAATATATTATTAATTGA
1 ATAAATTTTTAAAATATAAAAATATATTATTAATTGA
*
1266752 ATAAATTTTTAAAATATAAAAGTATATTATTAATTGA
1 ATAAATTTTTAAAATATAAAAATATATTATTAATTGA
1266789 A
1 A
1266790 AATATAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (37 bp):
ATAAATTTTTAAAATATAAAAATATATTATTAATTGA
Found at i:1278866 original size:31 final size:29
Alignment explanation
Indices: 1278831--1278894 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
1278821 GTCAAGTCTT
*
1278831 ACGTGTCCAAAATATTGATGTTGATATTGTC
1 ACGTGTCCAAAATA-TGATG-TAATATTGTC
** *
1278862 ACGTGTGTAAAGTATGATGTAATATTGTC
1 ACGTGTCCAAAATATGATGTAATATTGTC
1278891 ACGT
1 ACGT
1278895 CATCATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 13 0.45
30 5 0.17
31 11 0.38
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (29 bp):
ACGTGTCCAAAATATGATGTAATATTGTC
Found at i:1284346 original size:60 final size:61
Alignment explanation
Indices: 1284279--1284441 Score: 163
Period size: 60 Copynumber: 2.7 Consensus size: 61
1284269 AAATGTGTCT
*
1284279 AAAAGTTTGGGGATCAATTTATAACGAAGATCATAGTTTGAG-GAAGAAAATGAAATATTC
1 AAAAGTTTGGGGATCAATTTATAATGAAGATCATAGTTTGAGAGAAGAAAATGAAATATTC
** * * * * *
1284339 AAAAGTTTGAAGATTAATTTAGAATGATAG-TCATAGTTT-AGAGATGAAATTGAAATATTT
1 AAAAGTTTGGGGATCAATTTATAATGA-AGATCATAGTTTGAGAGAAGAAAATGAAATATTC
* * * * *
1284399 AAAACTTTAGGGA-CTAATTTATAATAAAAATCATAATTTGAGA
1 AAAAGTTTGGGGATC-AATTTATAATGAAGATCATAGTTTGAGA
1284442 ATATATGATA
Statistics
Matches: 81, Mismatches: 17, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
59 3 0.04
60 73 0.90
61 5 0.06
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.33
Consensus pattern (61 bp):
AAAAGTTTGGGGATCAATTTATAATGAAGATCATAGTTTGAGAGAAGAAAATGAAATATTC
Found at i:1289536 original size:34 final size:34
Alignment explanation
Indices: 1289493--1289582 Score: 137
Period size: 33 Copynumber: 2.7 Consensus size: 34
1289483 CCCAGGTGTA
*
1289493 AAGTTGGCCACCTACCAAAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
* * *
1289527 AAGTTGGCCACAAACC-AAGATTATTTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
1289560 AAGTTGGCCACCAACCAAAGATG
1 AAGTTGGCCACCAACCAAAGATG
1289583 TCAACTTTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
33 30 0.61
34 19 0.39
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (34 bp):
AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
Found at i:1294211 original size:33 final size:34
Alignment explanation
Indices: 1294152--1294241 Score: 128
Period size: 33 Copynumber: 2.7 Consensus size: 34
1294142 GCCATGTACA
* **
1294152 AAGTTGGCCACCTACCAAAGATGAATTTTTTAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
*
1294186 AAGTTGGTCACCAACC-AAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
*
1294219 AAGTTAGCCACCAACCAAAGATG
1 AAGTTGGCCACCAACCAAAGATG
1294242 TCAACTTTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
33 29 0.59
34 20 0.41
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.26
Consensus pattern (34 bp):
AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
Found at i:1299561 original size:22 final size:22
Alignment explanation
Indices: 1299536--1299598 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
1299526 AGTCGAGGGT
*
1299536 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCTTTCGGGACATA
1299558 TACATAGGTCTTTCGGGACATA
1 TACATAGGTCTTTCGGGACATA
1299580 T--ATGAGGTCTTTCGGGACA
1 TACAT-AGGTCTTTCGGGACA
1299599 AATTTCATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
20 2 0.05
21 15 0.38
22 22 0.56
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (22 bp):
TACATAGGTCTTTCGGGACATA
Found at i:1299882 original size:18 final size:18
Alignment explanation
Indices: 1299847--1299890 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1299837 GAGAGATACG
**
1299847 AATGATAACAATGTTAAT
1 AATGATAACAATAATAAT
*
1299865 AATGATAAGAATAATAAT
1 AATGATAACAATAATAAT
*
1299883 AAGGATAA
1 AATGATAA
1299891 TGATGTTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.57, C:0.02, G:0.14, T:0.27
Consensus pattern (18 bp):
AATGATAACAATAATAAT
Found at i:1305551 original size:85 final size:85
Alignment explanation
Indices: 1305408--1305906 Score: 662
Period size: 85 Copynumber: 5.9 Consensus size: 85
1305398 ATCTCCCAGC
* * *
1305408 CAAATTTACAGTATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTA
1 CAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTCGATTA
*
1305473 CATTCATCTCAAGGGCATAT
66 CATTCAGCTCAAGGGCATAT
* *
1305493 CAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTTGATTA
1 CAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTCGATTA
1305558 CATTCAGCTCAAGGGCATAT
66 CATTCAGCTCAAGGGCATAT
* * * * * * * * *
1305578 CAAATTTACAGTATAGCTCAAAGTGAGAATGGCTATCTGTCAACAAAAACCTCCAAGTTCAATTC
1 CAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTCGATTA
1305643 CATTCAGCTCAAGGGCATAT
66 CATTCAGCTCAAGGGCATAT
* * * * *
1305663 CAAATTTACAGCATAACTCAAGGCGAGAAAGGCTATATGTTAA-AAAAACTTTCGAGTTCGATTC
1 CAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTCGATTA
1305727 CATTCAGCTCAAGGGCATAT
66 CATTCAGCTCAAGGGCATAT
* * * * * *
1305747 TAAATTTATAGCATAGTTCAAGGCGAGAAGGGTTATCTGTTAACAAAAACCTTCGAGTTCGATT-
1 CAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTCGATTA
* *
1305811 CAACTCAGCTCAAGGGCATAA
66 C-ATTCAGCTCAAGGGCATAT
* * ** *
1305832 CAAATTTATAGCATAGCTCAAGGCGAGAAGGGTTATATGTCAATGAAAACTTTCGAGTTCGATT-
1 CAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTCGATTA
1305896 CTATTCAGCTC
66 C-ATTCAGCTC
1305907 GATGACATAT
Statistics
Matches: 365, Mismatches: 47, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
84 74 0.20
85 291 0.80
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (85 bp):
CAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTCGATTA
CATTCAGCTCAAGGGCATAT
Found at i:1305690 original size:170 final size:168
Alignment explanation
Indices: 1305408--1305906 Score: 710
Period size: 169 Copynumber: 2.9 Consensus size: 168
1305398 ATCTCCCAGC
* *
1305408 CAAATTTACAGTATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTA
1 CAAATTTACAGTATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTC
* *
1305473 CATTCATCTCAAGGGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATATGTCAACA
66 CATTCAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATATGTCAA-A
* *
1305538 AAAACCTTCGAGTTTGATTACATTCAGCTCAAGGGCATAT
130 AAAACTTTCGAGTTCGATT-CATTCAGCTCAAGGGCATAT
* * * * * *
1305578 CAAATTTACAGTATAGCTCAAAGTGAGAATGGCTATCTGTCAACAAAAACCTCCAAGTTCAATTC
1 CAAATTTACAGTATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTC
* * *
1305643 CATTCAGCTCAAGGGCATATCAAATTTACAGCATAACTCAAGGCGAGAAAGGCTATATGTTAAAA
66 CATTCAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATATGTCAAAA
1305708 AAACTTTCGAGTTCGATTCCATTCAGCTCAAGGGCATAT
131 AAACTTTCGAGTTCGATT-CATTCAGCTCAAGGGCATAT
* * * * * *
1305747 TAAATTTATAGCATAGTTCAAGGCGAGAAGGGTTATCTGTTAACAAAAACCTTCGAGTTCGATTC
1 CAAATTTACAGTATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTC
* * * * * *
1305812 AACTCAGCTCAAGGGCATAACAAATTTATAGCATAGCTCAAGGCGAGAAGGGTTATATGTCAATG
66 CATTCAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATATGTCAA-A
1305877 AAAACTTTCGAGTTCGATTCTATTCAGCTC
130 AAAACTTTCGAGTTCGATTC-ATTCAGCTC
1305907 GATGACATAT
Statistics
Matches: 290, Mismatches: 37, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
169 147 0.51
170 143 0.49
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (168 bp):
CAAATTTACAGTATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTC
CATTCAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATATGTCAAAA
AAACTTTCGAGTTCGATTCATTCAGCTCAAGGGCATAT
Found at i:1305904 original size:254 final size:255
Alignment explanation
Indices: 1305408--1305906 Score: 696
Period size: 254 Copynumber: 2.0 Consensus size: 255
1305398 ATCTCCCAGC
* * *
1305408 CAAATTTACAGTATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTA
1 CAAATTTACAGCATAACTCAAGGCGAGAAAGGCTATATGTCAACAAAAACCTTCGAGTTCGATTA
*
1305473 CATTCATCTCAAGGGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATATGTCAACA
66 CATTCAGCTCAAGGGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATATGTCAACA
* * * * *
1305538 AAAACCTTCGAGTTTGATTACATTCAGCTCAAGGGCATATCAAATTTACAGTATAGCTCAAAGTG
131 AAAACCTTCGAGTTCGATTACACTCAGCTCAAGGGCATAACAAATTTACAGCATAGCTCAAAGCG
* *
1305603 AGAATGGCTATCTGTCAACAAAAACCTCCAAGTTCAATTCCATTCAGCTCAAGGGCATAT
196 AGAAGGGCTATATGTCAACAAAAACCTCCAAGTTCAATTCCATTCAGCTCAAGGGCATAT
* * *
1305663 CAAATTTACAGCATAACTCAAGGCGAGAAAGGCTATATGTTAA-AAAAACTTTCGAGTTCGATTC
1 CAAATTTACAGCATAACTCAAGGCGAGAAAGGCTATATGTCAACAAAAACCTTCGAGTTCGATTA
* * * * * * *
1305727 CATTCAGCTCAAGGGCATATTAAATTTATAGCATAGTTCAAGGCGAGAAGGGTTATCTGTTAACA
66 CATTCAGCTCAAGGGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATATGTCAACA
* *
1305792 AAAACCTTCGAGTTCGATT-CAACTCAGCTCAAGGGCATAACAAATTTATAGCATAGCTCAAGGC
131 AAAACCTTCGAGTTCGATTAC-ACTCAGCTCAAGGGCATAACAAATTTACAGCATAGCTCAAAGC
* ** * * * * *
1305856 GAGAAGGGTTATATGTCAATGAAAACTTTCGAGTTCGATTCTATTCAGCTC
195 GAGAAGGGCTATATGTCAACAAAAACCTCCAAGTTCAATTCCATTCAGCTC
1305907 GATGACATAT
Statistics
Matches: 212, Mismatches: 31, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
253 1 0.00
254 172 0.81
255 39 0.18
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (255 bp):
CAAATTTACAGCATAACTCAAGGCGAGAAAGGCTATATGTCAACAAAAACCTTCGAGTTCGATTA
CATTCAGCTCAAGGGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATATGTCAACA
AAAACCTTCGAGTTCGATTACACTCAGCTCAAGGGCATAACAAATTTACAGCATAGCTCAAAGCG
AGAAGGGCTATATGTCAACAAAAACCTCCAAGTTCAATTCCATTCAGCTCAAGGGCATAT
Found at i:1306736 original size:38 final size:40
Alignment explanation
Indices: 1306689--1306773 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 40
1306679 CAAAAAATAA
* *
1306689 ATAACATATAG-TTTTTAGAAAA-CGGTTATTGAAAACAT
1 ATAATATATAGTTTTTTAAAAAATCGGTTATTGAAAACAT
* *
1306727 ATAATATATAGTTTTTTAAAAAATCGGTTTTTGAAAATAT
1 ATAATATATAGTTTTTTAAAAAATCGGTTATTGAAAACAT
1306767 ATAATAT
1 ATAATAT
1306774 GGTTTTGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 10 0.24
39 10 0.24
40 21 0.51
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.40
Consensus pattern (40 bp):
ATAATATATAGTTTTTTAAAAAATCGGTTATTGAAAACAT
Found at i:1306837 original size:2 final size:2
Alignment explanation
Indices: 1306830--1306862 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1306820 ACAATTTTTA
1306830 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1306863 GTTTTGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1306861 original size:57 final size:55
Alignment explanation
Indices: 1306799--1306956 Score: 177
Period size: 55 Copynumber: 2.9 Consensus size: 55
1306789 ATATAAAAAC
1306799 ATATAT-TATAT-TGTTTTAAAAACAATTTTT--AATATATATATATATATATAT
1 ATATATATATATATGTTTTAAAAACAATTTTTAAAATATATATATATATATATAT
* ** *
1306850 ATATATATATATA-GTTTTGAAAACGGTTTTAGAAAATATATATATATATATATAT
1 ATATATATATATATGTTTTAAAAACAATTTT-TAAAATATATATATATATATATAT
* * *
1306905 ATATATATATATATAGTTTTTAAAA-TATTTTTGAAAACATATATATA-ATATA
1 ATATATATATATAT-GTTTTAAAAACAATTTTT-AAAATATATATATATATATA
1306957 GGTTTGAAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
51 6 0.07
52 19 0.21
55 39 0.43
56 17 0.19
57 9 0.10
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (55 bp):
ATATATATATATATGTTTTAAAAACAATTTTTAAAATATATATATATATATATAT
Found at i:1306892 original size:2 final size:2
Alignment explanation
Indices: 1306885--1306919 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1306875 GTTTTAGAAA
1306885 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1306920 GTTTTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1306978 original size:14 final size:14
Alignment explanation
Indices: 1306959--1306985 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1306949 ATAATATAGG
1306959 TTTGAAAACATATT
1 TTTGAAAACATATT
1306973 TTTGAAAACATAT
1 TTTGAAAACATAT
1306986 AATATATAGT
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:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
TTTGAAAACATATT
Found at i:1306986 original size:37 final size:37
Alignment explanation
Indices: 1306907--1307025 Score: 143
Period size: 39 Copynumber: 3.1 Consensus size: 37
1306897 ATATATATAT
*
1306907 ATATATATATATA-GTTTTTAAAATATTTTTGAAAAC
1 ATATATATATATAGGTTTTAAAAATATTTTTGAAAAC
*
1306943 ATATATATAATATAGGTTTGAAAACATATTTTTGAAAAC
1 ATATATAT-ATATAGGTTTTAAAA-ATATTTTTGAAAAC
* *
1306982 ATATA-ATATATAGTTTTTTAAAAAATGATTTTTTAAAAC
1 ATATATATATATAG-GTTTT-AAAAAT-ATTTTTGAAAAC
1307021 ATATA
1 ATATA
1307026 GTTTTGGAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
36 8 0.11
37 11 0.15
38 14 0.19
39 39 0.54
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (37 bp):
ATATATATATATAGGTTTTAAAAATATTTTTGAAAAC
Found at i:1307621 original size:25 final size:26
Alignment explanation
Indices: 1307570--1307625 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
1307560 AAACTAAGCA
* *
1307570 AAGAAATGCATAACAAACAATCAAAC
1 AAGAAATGCAAAACAAAAAATCAAAC
1307596 AAGAAA-GCAAAACAAGAAAATC-AAC
1 AAGAAATGCAAAACAA-AAAATCAAAC
1307621 AAGAA
1 AAGAA
1307626 CGTTTCACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.66, C:0.16, G:0.11, T:0.07
Consensus pattern (26 bp):
AAGAAATGCAAAACAAAAAATCAAAC
Done.